From 22b9b33dd96d4e7a5b47895f663c419e55b76b4b Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Tue, 13 Aug 2024 14:58:48 -0400
Subject: [PATCH 01/19] clean up some elements

---
 .../model/petrinet/tera-parameter-table.vue   | 26 ++++++++++++-------
 .../tera-model-config-drilldown.vue           |  1 -
 2 files changed, 16 insertions(+), 11 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 10baeaef92..6505f8693b 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
@@ -73,12 +73,12 @@
 												@update-source="emit('update-source', $event)"
 											/>
 										</div>
-										<Divider type="solid" />
 									</li>
 								</ul>
 							</div>
 						</AccordionTab>
 					</Accordion>
+
 					<!-- Unstratified -->
 					<div v-else class="flex gap-4">
 						<Checkbox
@@ -99,7 +99,6 @@
 							@update-source="emit('update-source', $event)"
 						/>
 					</div>
-					<Divider type="solid" />
 				</li>
 			</ul>
 		</AccordionTab>
@@ -236,28 +235,35 @@ const onUpdateDistributions = () => {
 <style scoped>
 ul {
 	flex-grow: 1;
+
 	li {
 		list-style: none;
 	}
+
+	li + li {
+		border-top: 1px solid var(--gray-300);
+		margin-top: var(--gap-1-5);
+		padding-top: var(--gap-4);
+	}
+
+	li:last-child {
+		margin-bottom: var(--gap-4);
+	}
 }
 
 :deep(.p-divider) {
-	&.p-divider-horizontal {
-		margin-top: 0;
-		margin-bottom: var(--gap);
-		color: var(--gray-300);
-	}
 	&.p-divider-vertical {
-		margin-left: var(--gap-small);
-		margin-right: var(--gap);
+		margin-left: var(--gap-2);
+		margin-right: var(--gap-4);
 	}
 }
 
 .artifact-amount {
 	font-size: var(--font-caption);
 	color: var(--text-color-subdued);
-	margin-left: 0.25rem;
+	margin-left: var(--gap-1);
 }
+
 :deep(.uncertainty-percentage) > input {
 	width: 4rem;
 }
diff --git a/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config-drilldown.vue b/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config-drilldown.vue
index 5a1c84a511..1413ce0f01 100644
--- a/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config-drilldown.vue
+++ b/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config-drilldown.vue
@@ -75,7 +75,6 @@
 				<Button label="Reset" @click="resetConfiguration" outlined severity="secondary" />
 				<Button class="mr-3" :disabled="isSaveDisabled" label="Save" @click="() => createConfiguration()" />
 			</template>
-
 			<Accordion multiple :active-index="[0, 1]">
 				<AccordionTab>
 					<template #header>

From 24ba8ffa6d665e40f6cef2467f714275ae1ac31b Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Tue, 13 Aug 2024 15:29:47 -0400
Subject: [PATCH 02/19] remove the divider and some clean up

---
 .../model/petrinet/tera-parameter-table.vue   | 52 ++++++++++---------
 1 file changed, 27 insertions(+), 25 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 6505f8693b..5c20e4529c 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
@@ -50,29 +50,26 @@
 								<span>{{ baseParameter }}</span>
 								<Button label="Open Matrix" text size="small" @click.stop="matrixModalId = baseParameter" />
 							</template>
-							<div class="flex">
-								<Divider layout="vertical" type="solid" />
+							<div class="stratified">
 								<ul>
 									<li v-for="{ referenceId } in childParameters" :key="referenceId">
-										<div class="flex gap-4">
-											<Checkbox
-												v-if="
-													isAddingUncertainty &&
-													getParameterDistribution(modelConfiguration, referenceId).type === DistributionType.Constant
-												"
-												binary
-												:model-value="selectedParameters.includes(referenceId)"
-												@change="onSelect(referenceId)"
-											/>
-											<tera-parameter-entry
-												:model="model"
-												:model-configuration="props.modelConfiguration"
-												:model-configurations="props.modelConfigurations"
-												:parameter-id="referenceId"
-												@update-parameter="emit('update-parameters', [$event])"
-												@update-source="emit('update-source', $event)"
-											/>
-										</div>
+										<Checkbox
+											v-if="
+												isAddingUncertainty &&
+												getParameterDistribution(modelConfiguration, referenceId).type === DistributionType.Constant
+											"
+											binary
+											:model-value="selectedParameters.includes(referenceId)"
+											@change="onSelect(referenceId)"
+										/>
+										<tera-parameter-entry
+											:model="model"
+											:model-configuration="props.modelConfiguration"
+											:model-configurations="props.modelConfigurations"
+											:parameter-id="referenceId"
+											@update-parameter="emit('update-parameters', [$event])"
+											@update-source="emit('update-source', $event)"
+										/>
 									</li>
 								</ul>
 							</div>
@@ -136,7 +133,6 @@ import { MiraModel, MiraTemplateParams } from '@/model-representation/mira/mira-
 import Accordion from 'primevue/accordion';
 import AccordionTab from 'primevue/accordiontab';
 import Button from 'primevue/button';
-import Divider from 'primevue/divider';
 import { DistributionType, DistributionTypeLabel, distributionTypeOptions } from '@/services/distribution';
 import InputNumber from 'primevue/inputnumber';
 import Dropdown from 'primevue/dropdown';
@@ -251,10 +247,16 @@ ul {
 	}
 }
 
-:deep(.p-divider) {
-	&.p-divider-vertical {
+.stratified {
+	ul {
+		border-left: 1px solid var(--gray-300);
 		margin-left: var(--gap-2);
-		margin-right: var(--gap-4);
+		padding-left: var(--gap-4);
+	}
+
+	li {
+		display: flex;
+		gap: var(--gap-4);
 	}
 }
 

From ac3be57dc379c1055cc4bfcc595f06d6367898a4 Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 11:34:26 -0400
Subject: [PATCH 03/19] Update service to fetch provenance for model
 configuration extracted from

---
 .../service/data/ProvenanceSearchService.java | 43 ++++++++++++++++++-
 1 file changed, 42 insertions(+), 1 deletion(-)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java
index 0ee4c59edf..f19aaf213f 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java
@@ -17,6 +17,7 @@
 import org.neo4j.driver.types.Node;
 import org.neo4j.driver.types.Relationship;
 import org.springframework.stereotype.Service;
+import software.uncharted.terarium.hmiserver.models.dataservice.provenance.Provenance;
 import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceEdge;
 import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceNode;
 import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceQueryParam;
@@ -96,6 +97,46 @@ public ProvenanceSearchResult concept(final ProvenanceQueryParam payload) {
 		}
 	}
 
+	/**
+	 * Get the documents and datasets used to create a model configuration
+	 *
+	 * @param model-configuration-id - Model configuration id.
+	 * @return Set<Provenance> - The Documents and Datasets used to create a model configuration.
+	 */
+	public Set<Provenance> modelConfigSource(final UUID modelConfigurationId) {
+		final Set<Provenance> provenances = new HashSet<>();
+		try (final Session session = neo4jService.getSession()) {
+			final String documentsQuery = String.format(
+				"MATCH (d:Document)<-[r:EXTRACTED_FROM]-(m:ModelConfiguration {id: '%s'}) RETURN d " + modelConfigurationId
+			);
+
+			final Result documentResponse = session.run(documentsQuery);
+			while (documentResponse.hasNext()) {
+				final Provenance provenance = new Provenance();
+				provenance.setLeft(modelConfigurationId);
+				provenance.setRight(UUID.fromString(documentResponse.next().get("d").get("id").asString()));
+				provenance.setRightType(ProvenanceType.DOCUMENT);
+				provenance.setRelationType(ProvenanceRelationType.EXTRACTED_FROM);
+				provenances.add(provenance);
+			}
+
+			final String datasetsQuery = String.format(
+				"MATCH (ds:Dataset)<-[r:EXTRACTED_FROM]-(m:ModelConfiguration {id: '%s'}) RETURN ds",
+				modelConfigurationId
+			);
+			final Result datasetResponse = session.run(datasetsQuery);
+			while (datasetResponse.hasNext()) {
+				final Provenance provenance = new Provenance();
+				provenance.setLeft(modelConfigurationId);
+				provenance.setRight(UUID.fromString(datasetResponse.next().get("d").get("id").asString()));
+				provenance.setRightType(ProvenanceType.DATASET);
+				provenance.setRelationType(ProvenanceRelationType.EXTRACTED_FROM);
+				provenances.add(provenance);
+			}
+			return provenances;
+		}
+	}
+
 	/**
 	 * Identifies the document from which a model configuration was extracted
 	 *
@@ -105,7 +146,7 @@ public ProvenanceSearchResult concept(final ProvenanceQueryParam payload) {
 	public Set<String> modelConfigFromDocument(final ProvenanceQueryParam payload) {
 		if (payload.getRootType() != ProvenanceType.MODEL_CONFIGURATION) {
 			throw new IllegalArgumentException(
-				"Document used for model-configuration extraction can only be found by providing a model-confirguration"
+				"Document used for model-configuration extraction can only be found by providing a model-configuration"
 			);
 		}
 

From de11ca37eea1272c7785941e965858044d5a1609 Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 11:49:08 -0400
Subject: [PATCH 04/19] improve the provenance call

---
 .../service/data/ProvenanceSearchService.java | 41 ++++++++-----------
 1 file changed, 18 insertions(+), 23 deletions(-)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java
index f19aaf213f..b99b775871 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java
@@ -100,36 +100,31 @@ public ProvenanceSearchResult concept(final ProvenanceQueryParam payload) {
 	/**
 	 * Get the documents and datasets used to create a model configuration
 	 *
-	 * @param model-configuration-id - Model configuration id.
+	 * @param id - Model configuration id.
 	 * @return Set<Provenance> - The Documents and Datasets used to create a model configuration.
 	 */
-	public Set<Provenance> modelConfigSource(final UUID modelConfigurationId) {
+	public Set<Provenance> modelConfigSource(final UUID id) {
 		final Set<Provenance> provenances = new HashSet<>();
 		try (final Session session = neo4jService.getSession()) {
-			final String documentsQuery = String.format(
-				"MATCH (d:Document)<-[r:EXTRACTED_FROM]-(m:ModelConfiguration {id: '%s'}) RETURN d " + modelConfigurationId
+			final String query = String.format(
+				"MATCH (d:Document)<-[r:EXTRACTED_FROM]-(m:ModelConfiguration {id: '%s'}) RETURN d.id as id, 'DOCUMENT' as type " +
+				"UNION " +
+				"MATCH (ds:Dataset)<-[r:EXTRACTED_FROM]-(m:ModelConfiguration {id: '%s'}) RETURN ds.id as id, 'DATASET' as type",
+				id,
+				id
 			);
 
-			final Result documentResponse = session.run(documentsQuery);
-			while (documentResponse.hasNext()) {
-				final Provenance provenance = new Provenance();
-				provenance.setLeft(modelConfigurationId);
-				provenance.setRight(UUID.fromString(documentResponse.next().get("d").get("id").asString()));
-				provenance.setRightType(ProvenanceType.DOCUMENT);
-				provenance.setRelationType(ProvenanceRelationType.EXTRACTED_FROM);
-				provenances.add(provenance);
-			}
-
-			final String datasetsQuery = String.format(
-				"MATCH (ds:Dataset)<-[r:EXTRACTED_FROM]-(m:ModelConfiguration {id: '%s'}) RETURN ds",
-				modelConfigurationId
-			);
-			final Result datasetResponse = session.run(datasetsQuery);
-			while (datasetResponse.hasNext()) {
+			final Result response = session.run(query);
+			while (response.hasNext()) {
+				final var record = response.next();
+				final ProvenanceType recordType = record.get("type").asString().equals("DOCUMENT")
+					? ProvenanceType.DOCUMENT
+					: ProvenanceType.DATASET;
 				final Provenance provenance = new Provenance();
-				provenance.setLeft(modelConfigurationId);
-				provenance.setRight(UUID.fromString(datasetResponse.next().get("d").get("id").asString()));
-				provenance.setRightType(ProvenanceType.DATASET);
+				provenance.setLeft(id);
+				provenance.setLeftType(ProvenanceType.MODEL_CONFIGURATION);
+				provenance.setRight(UUID.fromString(record.get("id").asString()));
+				provenance.setRightType(recordType);
 				provenance.setRelationType(ProvenanceRelationType.EXTRACTED_FROM);
 				provenances.add(provenance);
 			}

From f9ea6cb065a4114492659bcd906c0d2d99a21ba7 Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 12:48:10 -0400
Subject: [PATCH 05/19] Add endpoint

---
 .../ModelConfigurationController.java         | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
index 327713c982..72c9cb66e2 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
@@ -7,8 +7,10 @@
 import io.swagger.v3.oas.annotations.responses.ApiResponse;
 import io.swagger.v3.oas.annotations.responses.ApiResponses;
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
+import java.util.Set;
 import java.util.UUID;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
@@ -28,11 +30,17 @@
 import software.uncharted.terarium.hmiserver.models.dataservice.ResponseDeleted;
 import software.uncharted.terarium.hmiserver.models.dataservice.model.Model;
 import software.uncharted.terarium.hmiserver.models.dataservice.model.configurations.ModelConfiguration;
+import software.uncharted.terarium.hmiserver.models.dataservice.provenance.Provenance;
+import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceQueryParam;
+import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceRelationType;
+import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceType;
 import software.uncharted.terarium.hmiserver.security.Roles;
 import software.uncharted.terarium.hmiserver.service.CurrentUserService;
 import software.uncharted.terarium.hmiserver.service.data.ModelConfigurationService;
 import software.uncharted.terarium.hmiserver.service.data.ModelService;
 import software.uncharted.terarium.hmiserver.service.data.ProjectService;
+import software.uncharted.terarium.hmiserver.service.data.ProvenanceSearchService;
+import software.uncharted.terarium.hmiserver.service.data.ProvenanceService;
 import software.uncharted.terarium.hmiserver.utils.Messages;
 import software.uncharted.terarium.hmiserver.utils.rebac.Schema.Permission;
 
@@ -47,6 +55,7 @@ public class ModelConfigurationController {
 	final CurrentUserService currentUserService;
 	final Messages messages;
 	final ProjectService projectService;
+	final ProvenanceSearchService provenanceSearchService;
 
 	/**
 	 * Gets all model configurations (which are visible to this user)
@@ -154,6 +163,42 @@ public ResponseEntity<ModelConfiguration> getModelConfiguration(
 		}
 	}
 
+	/**
+	 * Gets all the Document and Dataset provenance from a model configuration
+	 *
+	 * @param id UUID of the model configuration
+	 * @return the list of asset ids and types
+	 */
+	@GetMapping("/{id}/extracted-from")
+	@Secured(Roles.USER)
+	@Operation(summary = "Gets all the Document and Dataset provenance from a model configuration")
+	@ApiResponses(
+		value = {
+			@ApiResponse(
+				responseCode = "200",
+				description = "Provenances found.",
+				content = @Content(array = @ArraySchema(schema = @Schema(implementation = Provenance.class)))
+			),
+			@ApiResponse(
+				responseCode = "503",
+				description = "There was an issue communicating with back-end services",
+				content = @Content
+			)
+		}
+	)
+	public ResponseEntity<Set<Provenance>> getExtractedFrom(@PathVariable("id") final UUID id) {
+		try {
+			final Set<Provenance> provenances = provenanceSearchService.modelConfigSource(id);
+			return ResponseEntity.ok(provenances);
+		} catch (final Exception e) {
+			log.error("Unable to get model0configuration extraction source from the neo4j db", e);
+			throw new ResponseStatusException(
+				org.springframework.http.HttpStatus.SERVICE_UNAVAILABLE,
+				messages.get("neo4j.service-unavailable")
+			);
+		}
+	}
+
 	/**
 	 * Create a configured model from a model config
 	 *

From f9e81261e902efb40d66d7c6794a0765c337139b Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 12:54:26 -0400
Subject: [PATCH 06/19] random cleaning up

---
 .../ModelConfigurationController.java         |  5 --
 .../service/data/ProvenanceSearchService.java | 78 +------------------
 2 files changed, 2 insertions(+), 81 deletions(-)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
index 72c9cb66e2..73251817ec 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
@@ -7,7 +7,6 @@
 import io.swagger.v3.oas.annotations.responses.ApiResponse;
 import io.swagger.v3.oas.annotations.responses.ApiResponses;
 import java.io.IOException;
-import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
@@ -31,16 +30,12 @@
 import software.uncharted.terarium.hmiserver.models.dataservice.model.Model;
 import software.uncharted.terarium.hmiserver.models.dataservice.model.configurations.ModelConfiguration;
 import software.uncharted.terarium.hmiserver.models.dataservice.provenance.Provenance;
-import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceQueryParam;
-import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceRelationType;
-import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceType;
 import software.uncharted.terarium.hmiserver.security.Roles;
 import software.uncharted.terarium.hmiserver.service.CurrentUserService;
 import software.uncharted.terarium.hmiserver.service.data.ModelConfigurationService;
 import software.uncharted.terarium.hmiserver.service.data.ModelService;
 import software.uncharted.terarium.hmiserver.service.data.ProjectService;
 import software.uncharted.terarium.hmiserver.service.data.ProvenanceSearchService;
-import software.uncharted.terarium.hmiserver.service.data.ProvenanceService;
 import software.uncharted.terarium.hmiserver.utils.Messages;
 import software.uncharted.terarium.hmiserver.utils.rebac.Schema.Permission;
 
diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java
index b99b775871..73cd16c382 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java
@@ -132,66 +132,6 @@ final var record = response.next();
 		}
 	}
 
-	/**
-	 * Identifies the document from which a model configuration was extracted
-	 *
-	 * @param payload - Search param payload.
-	 * @return
-	 */
-	public Set<String> modelConfigFromDocument(final ProvenanceQueryParam payload) {
-		if (payload.getRootType() != ProvenanceType.MODEL_CONFIGURATION) {
-			throw new IllegalArgumentException(
-				"Document used for model-configuration extraction can only be found by providing a model-configuration"
-			);
-		}
-
-		try (final Session session = neo4jService.getSession()) {
-			final UUID modelConfigurationId = payload.getRootId();
-
-			final String query = String.format(
-				"MATCH (d:Document)<-[r:EXTRACTED_FROM]-(m:ModelConfiguration {id: '%s'}) RETURN d",
-				modelConfigurationId
-			);
-
-			final Result response = session.run(query);
-			final Set<String> responseData = new HashSet<>();
-			while (response.hasNext()) {
-				responseData.add(response.next().get("d").get("id").asString());
-			}
-			return responseData;
-		}
-	}
-
-	/**
-	 * Identifies the dataset from which a model configuration was extracted
-	 *
-	 * @param payload - Search param payload.
-	 * @return
-	 */
-	public Set<String> modelConfigFromDataset(final ProvenanceQueryParam payload) {
-		if (payload.getRootType() != ProvenanceType.MODEL_CONFIGURATION) {
-			throw new IllegalArgumentException(
-				"Dataset used for model-configuration extraction can only be found by providing a model-confirguration"
-			);
-		}
-
-		try (final Session session = neo4jService.getSession()) {
-			final UUID modelConfigurationId = payload.getRootId();
-
-			final String query = String.format(
-				"MATCH (d:Dataset)<-[r:EXTRACTED_FROM]-(m:ModelConfiguration {id: '%s'}) RETURN d",
-				modelConfigurationId
-			);
-
-			final Result response = session.run(query);
-			final Set<String> responseData = new HashSet<>();
-			while (response.hasNext()) {
-				responseData.add(response.next().get("d").get("id").asString());
-			}
-			return responseData;
-		}
-	}
-
 	/**
 	 * Identifies the document from which a model was extracted
 	 *
@@ -294,7 +234,7 @@ public static List<ProvenanceEdge> filterRelationshipTypes(
 		final List<ProvenanceEdge> relationships,
 		final List<ProvenanceType> includedTypes
 	) {
-		if (includedTypes.size() == 0) {
+		if (includedTypes.isEmpty()) {
 			return relationships;
 		}
 		final List<ProvenanceEdge> clipped = new ArrayList<>();
@@ -312,7 +252,7 @@ public static List<ProvenanceNode> filterNodeTypes(
 		final List<ProvenanceNode> nodes,
 		final List<ProvenanceType> includedTypes
 	) {
-		if (includedTypes.size() == 0) {
+		if (includedTypes.isEmpty()) {
 			return nodes;
 		}
 		final List<ProvenanceNode> res = new ArrayList<>();
@@ -337,25 +277,11 @@ public static List<ProvenanceNode> formattedNodes(final Graph graph) {
 				nodes.add(formatted);
 			} catch (final NoSuchElementException e) {
 				log.warn("No element found: " + e);
-				continue;
 			}
 		}
 		return nodes;
 	}
 
-	public static String dynamicRelationshipDirection(final String direction, final String relationshipType) {
-		switch (direction) {
-			case "all":
-				return String.format("-['%s']-", relationshipType);
-			case "child":
-				return String.format("<-['%s']-", relationshipType);
-			case "parent":
-				return String.format("-['%s']->", relationshipType);
-			default:
-				throw new IllegalArgumentException("Relationship direction is not allowed.");
-		}
-	}
-
 	public String matchNodeBuilder(final ProvenanceType nodeType) {
 		final String nodeTypeCharacter = returnNodeAbbr(nodeType);
 		return String.format("MATCH (%s:%s)", nodeTypeCharacter, nodeType);

From 9bce3f2e8d9a7d5386d8eb13ccb6f2628ace540f Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 13:48:30 -0400
Subject: [PATCH 07/19] Add service endpoint

---
 .../hmi-client/src/services/model-configurations.ts       | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/client/hmi-client/src/services/model-configurations.ts b/packages/client/hmi-client/src/services/model-configurations.ts
index 8ce6dab0bf..775e8bcec3 100644
--- a/packages/client/hmi-client/src/services/model-configurations.ts
+++ b/packages/client/hmi-client/src/services/model-configurations.ts
@@ -5,7 +5,8 @@ import type {
 	ModelConfiguration,
 	ModelDistribution,
 	ObservableSemantic,
-	ParameterSemantic
+	ParameterSemantic,
+	Provenance
 } from '@/types/Types';
 import { isEmpty } from 'lodash';
 import { pythonInstance } from '@/python/PyodideController';
@@ -68,6 +69,11 @@ export const getModelIdFromModelConfigurationId = async (id: string) => {
 	return modelConfiguration?.modelId ?? null;
 };
 
+export async function getExtractedFromSource(id: string): Promise<Provenance[]> {
+	const response = await API.get(`/model-configurations/${id}/extracted-from`);
+	return response?.data ?? ([] as Provenance[]);
+}
+
 export function getParameters(config: ModelConfiguration): ParameterSemantic[] {
 	return config.parameterSemanticList ?? [];
 }

From 8e7db0a7f8bccadc25bf11b9d3e5064d5d338a4a Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 14:16:06 -0400
Subject: [PATCH 08/19] Remove the front-end service

---
 .../hmi-client/src/services/model-configurations.ts       | 8 +-------
 .../dataservice/ModelConfigurationController.java         | 1 +
 .../model/configurations/ModelConfiguration.java          | 3 +--
 3 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/packages/client/hmi-client/src/services/model-configurations.ts b/packages/client/hmi-client/src/services/model-configurations.ts
index 775e8bcec3..8ce6dab0bf 100644
--- a/packages/client/hmi-client/src/services/model-configurations.ts
+++ b/packages/client/hmi-client/src/services/model-configurations.ts
@@ -5,8 +5,7 @@ import type {
 	ModelConfiguration,
 	ModelDistribution,
 	ObservableSemantic,
-	ParameterSemantic,
-	Provenance
+	ParameterSemantic
 } from '@/types/Types';
 import { isEmpty } from 'lodash';
 import { pythonInstance } from '@/python/PyodideController';
@@ -69,11 +68,6 @@ export const getModelIdFromModelConfigurationId = async (id: string) => {
 	return modelConfiguration?.modelId ?? null;
 };
 
-export async function getExtractedFromSource(id: string): Promise<Provenance[]> {
-	const response = await API.get(`/model-configurations/${id}/extracted-from`);
-	return response?.data ?? ([] as Provenance[]);
-}
-
 export function getParameters(config: ModelConfiguration): ParameterSemantic[] {
 	return config.parameterSemanticList ?? [];
 }
diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
index 73251817ec..5c6ee65c08 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
@@ -148,6 +148,7 @@ public ResponseEntity<ModelConfiguration> getModelConfiguration(
 			if (modelConfiguration.isEmpty()) {
 				throw new ResponseStatusException(HttpStatus.NOT_FOUND, messages.get("modelconfig.not-found"));
 			}
+
 			return ResponseEntity.ok(modelConfiguration.get());
 		} catch (final Exception e) {
 			log.error("Unable to get model configuration from postgres db", e);
diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/ModelConfiguration.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/ModelConfiguration.java
index 56741850c4..d33a97cdfb 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/ModelConfiguration.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/ModelConfiguration.java
@@ -44,8 +44,7 @@ public class ModelConfiguration extends TerariumAsset {
 	 * This field is only populated if simulationId is not null, it is meant as a sampling of the
 	 * configured space, but not necessarily the true distributions. It will set once and should
 	 * be readonly afterward.
-	 *
-	 * We will designated a dummy distribution type
+	 * We will designate a dummy distribution type
 	 * {
 	 *   type: 'inferred',
 	 *   parameters: {

From a705fdd699bdd5967ae5cdbbd70605ed0a6c17f0 Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 14:44:17 -0400
Subject: [PATCH 09/19] Add source to the configuration call

---
 .../tasks/ConfigureModelResponseHandler.java   | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureModelResponseHandler.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureModelResponseHandler.java
index 424caf0112..88b9d82001 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureModelResponseHandler.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureModelResponseHandler.java
@@ -3,20 +3,20 @@
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import java.util.List;
+import java.util.Objects;
 import java.util.UUID;
 import lombok.Data;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.stereotype.Component;
+import software.uncharted.terarium.hmiserver.configuration.Config;
 import software.uncharted.terarium.hmiserver.models.dataservice.model.Model;
 import software.uncharted.terarium.hmiserver.models.dataservice.model.configurations.ModelConfiguration;
-import software.uncharted.terarium.hmiserver.models.dataservice.modelparts.ModelParameter;
-import software.uncharted.terarium.hmiserver.models.dataservice.modelparts.semantics.Initial;
 import software.uncharted.terarium.hmiserver.models.dataservice.provenance.Provenance;
 import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceRelationType;
 import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceType;
 import software.uncharted.terarium.hmiserver.models.task.TaskResponse;
+import software.uncharted.terarium.hmiserver.service.data.DocumentAssetService;
 import software.uncharted.terarium.hmiserver.service.data.ModelConfigurationService;
 import software.uncharted.terarium.hmiserver.service.data.ModelService;
 import software.uncharted.terarium.hmiserver.service.data.ProvenanceService;
@@ -33,6 +33,8 @@ public class ConfigureModelResponseHandler extends TaskResponseHandler {
 	private final ModelService modelService;
 	private final ModelConfigurationService modelConfigurationService;
 	private final ProvenanceService provenanceService;
+	private final Config config;
+	private final DocumentAssetService documentAssetService;
 
 	@Override
 	public String getName() {
@@ -97,6 +99,16 @@ public TaskResponse onSuccess(final TaskResponse resp) {
 					condition.get("description").asText()
 				);
 
+				// Fetch the document name
+				final String documentName = Objects.requireNonNull(
+					documentAssetService.getAsset(props.documentId, ASSUME_WRITE_PERMISSION_ON_BEHALF_OF_USER).orElse(null)
+				).getName();
+
+				// Update the source of the model-configuration with the Document name
+				configuration.getInitialSemanticList().forEach(initial -> initial.setSource(documentName));
+				configuration.getParameterSemanticList().forEach(parameter -> parameter.setSource(documentName));
+				configuration.getObservableSemanticList().forEach(observable -> observable.setSource(documentName));
+
 				final ModelConfiguration newConfig = modelConfigurationService.createAsset(
 					configuration,
 					props.projectId,

From 7f49b89ea78865ab29a6164fa57521c9c61acf74 Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 14:59:14 -0400
Subject: [PATCH 10/19] improve the handler

---
 .../tasks/ConfigureModelResponseHandler.java    | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureModelResponseHandler.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureModelResponseHandler.java
index 88b9d82001..ec11063c93 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureModelResponseHandler.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureModelResponseHandler.java
@@ -4,12 +4,15 @@
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import java.util.Objects;
+import java.util.Optional;
 import java.util.UUID;
 import lombok.Data;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.stereotype.Component;
 import software.uncharted.terarium.hmiserver.configuration.Config;
+import software.uncharted.terarium.hmiserver.models.TerariumAsset;
+import software.uncharted.terarium.hmiserver.models.dataservice.document.DocumentAsset;
 import software.uncharted.terarium.hmiserver.models.dataservice.model.Model;
 import software.uncharted.terarium.hmiserver.models.dataservice.model.configurations.ModelConfiguration;
 import software.uncharted.terarium.hmiserver.models.dataservice.provenance.Provenance;
@@ -100,14 +103,16 @@ public TaskResponse onSuccess(final TaskResponse resp) {
 				);
 
 				// Fetch the document name
-				final String documentName = Objects.requireNonNull(
-					documentAssetService.getAsset(props.documentId, ASSUME_WRITE_PERMISSION_ON_BEHALF_OF_USER).orElse(null)
-				).getName();
+				final Optional<DocumentAsset> document = documentAssetService.getAsset(
+					props.documentId,
+					ASSUME_WRITE_PERMISSION_ON_BEHALF_OF_USER
+				);
+				final String source = document.map(TerariumAsset::getName).orElse(null);
 
 				// Update the source of the model-configuration with the Document name
-				configuration.getInitialSemanticList().forEach(initial -> initial.setSource(documentName));
-				configuration.getParameterSemanticList().forEach(parameter -> parameter.setSource(documentName));
-				configuration.getObservableSemanticList().forEach(observable -> observable.setSource(documentName));
+				configuration.getInitialSemanticList().forEach(initial -> initial.setSource(source));
+				configuration.getParameterSemanticList().forEach(parameter -> parameter.setSource(source));
+				configuration.getObservableSemanticList().forEach(observable -> observable.setSource(source));
 
 				final ModelConfiguration newConfig = modelConfigurationService.createAsset(
 					configuration,

From a4f212544ff3b98efb2241458fabeced89b2373e Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 14:59:20 -0400
Subject: [PATCH 11/19] Update the dataset extraction as well

---
 .../ConfigureFromDatasetResponseHandler.java  | 23 +++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
index 3ca89ccb10..ad163989f7 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
@@ -5,11 +5,15 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import java.io.IOException;
 import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
 import java.util.UUID;
 import lombok.Data;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.stereotype.Component;
+import software.uncharted.terarium.hmiserver.models.dataservice.dataset.Dataset;
+import software.uncharted.terarium.hmiserver.models.dataservice.document.DocumentAsset;
 import software.uncharted.terarium.hmiserver.models.dataservice.model.Model;
 import software.uncharted.terarium.hmiserver.models.dataservice.model.configurations.ModelConfiguration;
 import software.uncharted.terarium.hmiserver.models.dataservice.modelparts.ModelParameter;
@@ -18,6 +22,7 @@
 import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceRelationType;
 import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceType;
 import software.uncharted.terarium.hmiserver.models.task.TaskResponse;
+import software.uncharted.terarium.hmiserver.service.data.DatasetService;
 import software.uncharted.terarium.hmiserver.service.data.ModelConfigurationService;
 import software.uncharted.terarium.hmiserver.service.data.ModelService;
 import software.uncharted.terarium.hmiserver.service.data.ProvenanceService;
@@ -34,6 +39,7 @@ public class ConfigureFromDatasetResponseHandler extends TaskResponseHandler {
 	private final ModelService modelService;
 	private final ModelConfigurationService modelConfigurationService;
 	private final ProvenanceService provenanceService;
+	private final DatasetService datasetService;
 
 	@Override
 	public String getName() {
@@ -93,13 +99,26 @@ public TaskResponse onSuccess(final TaskResponse resp) {
 				modelCopy.getModel().put("initials", objectMapper.convertValue(modelInitials, JsonNode.class));
 			}
 
+			// Fetch the dataset names
+			final List<String> datasetsNames = List.of();
+			props.datasetIds.forEach(datasetId -> {
+				final Optional<Dataset> dataset = datasetService.getAsset(datasetId, ASSUME_WRITE_PERMISSION_ON_BEHALF_OF_USER);
+				dataset.ifPresent(value -> datasetsNames.add(value.getName()));
+			});
+			final String source = String.join(", ", datasetsNames);
+
 			// Create the new configuration
 			final ModelConfiguration modelConfiguration = ModelConfigurationService.modelConfigurationFromAMR(
 				modelCopy,
-				"New configuration from dataset",
-				""
+				"Configuration from dataset(s)",
+				"This configuration was created from the dataset(s): " + source
 			);
 
+			// Update the source of the model-configuration with the Document name
+			modelConfiguration.getInitialSemanticList().forEach(initial -> initial.setSource(source));
+			modelConfiguration.getParameterSemanticList().forEach(parameter -> parameter.setSource(source));
+			modelConfiguration.getObservableSemanticList().forEach(observable -> observable.setSource(source));
+
 			try {
 				for (final UUID datasetId : props.datasetIds) {
 					final ModelConfiguration newConfig = modelConfigurationService.createAsset(

From 3dbbd6c4ab590732460f6b6a4ac058c86641015b Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 15:17:27 -0400
Subject: [PATCH 12/19] Remove observables overwrites

---
 .../service/tasks/ConfigureFromDatasetResponseHandler.java       | 1 -
 .../hmiserver/service/tasks/ConfigureModelResponseHandler.java   | 1 -
 2 files changed, 2 deletions(-)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
index ad163989f7..132d3453a0 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
@@ -117,7 +117,6 @@ public TaskResponse onSuccess(final TaskResponse resp) {
 			// Update the source of the model-configuration with the Document name
 			modelConfiguration.getInitialSemanticList().forEach(initial -> initial.setSource(source));
 			modelConfiguration.getParameterSemanticList().forEach(parameter -> parameter.setSource(source));
-			modelConfiguration.getObservableSemanticList().forEach(observable -> observable.setSource(source));
 
 			try {
 				for (final UUID datasetId : props.datasetIds) {
diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureModelResponseHandler.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureModelResponseHandler.java
index ec11063c93..d3b9826ff1 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureModelResponseHandler.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureModelResponseHandler.java
@@ -112,7 +112,6 @@ public TaskResponse onSuccess(final TaskResponse resp) {
 				// Update the source of the model-configuration with the Document name
 				configuration.getInitialSemanticList().forEach(initial -> initial.setSource(source));
 				configuration.getParameterSemanticList().forEach(parameter -> parameter.setSource(source));
-				configuration.getObservableSemanticList().forEach(observable -> observable.setSource(source));
 
 				final ModelConfiguration newConfig = modelConfigurationService.createAsset(
 					configuration,

From 5e0a599f3de6b0c4eff49fb9ddb23eabd6bcae55 Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 15:17:48 -0400
Subject: [PATCH 13/19] Override setSource to add a source if not there.

---
 .../model/configurations/InitialSemantic.java         | 11 +++++++++++
 .../model/configurations/ParameterSemantic.java       | 11 +++++++++++
 2 files changed, 22 insertions(+)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/InitialSemantic.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/InitialSemantic.java
index a65f8d8deb..4b0db367c6 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/InitialSemantic.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/InitialSemantic.java
@@ -44,4 +44,15 @@ public InitialSemantic clone() {
 		clone.expressionMathml = this.expressionMathml;
 		return clone;
 	}
+
+	@Override
+	public void setSource(String source) {
+		if (this.getSource() != null) {
+			return;
+		}
+
+		if (this.expression != null || this.expressionMathml != null) {
+			super.setSource(source);
+		}
+	}
 }
diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/ParameterSemantic.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/ParameterSemantic.java
index ec0a82c641..7e78eae76e 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/ParameterSemantic.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/ParameterSemantic.java
@@ -46,4 +46,15 @@ public ParameterSemantic clone() {
 		clone.isDefault = this.isDefault;
 		return clone;
 	}
+
+	@Override
+	public void setSource(String source) {
+		if (this.getSource() != null) {
+			return;
+		}
+
+		if (!this.getDistribution().getParameters().isEmpty()) {
+			super.setSource(source);
+		}
+	}
 }

From 02d76b98307705bf5229930f9612634df1fa85cc Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 15:22:59 -0400
Subject: [PATCH 14/19] clean up

---
 .../ConfigureFromDatasetResponseHandler.java     | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
index 132d3453a0..8330599bde 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
@@ -4,8 +4,8 @@
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.List;
-import java.util.Objects;
 import java.util.Optional;
 import java.util.UUID;
 import lombok.Data;
@@ -13,7 +13,6 @@
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.stereotype.Component;
 import software.uncharted.terarium.hmiserver.models.dataservice.dataset.Dataset;
-import software.uncharted.terarium.hmiserver.models.dataservice.document.DocumentAsset;
 import software.uncharted.terarium.hmiserver.models.dataservice.model.Model;
 import software.uncharted.terarium.hmiserver.models.dataservice.model.configurations.ModelConfiguration;
 import software.uncharted.terarium.hmiserver.models.dataservice.modelparts.ModelParameter;
@@ -94,13 +93,18 @@ public TaskResponse onSuccess(final TaskResponse resp) {
 			final List<ModelParameter> modelParameters = ScenarioExtraction.getModelParameters(condition, modelCopy);
 			final List<Initial> modelInitials = ScenarioExtraction.getModelInitials(condition, modelCopy);
 
-			if (modelCopy.isRegnet()) {
-				modelCopy.getModel().put("parameters", objectMapper.convertValue(modelParameters, JsonNode.class));
-				modelCopy.getModel().put("initials", objectMapper.convertValue(modelInitials, JsonNode.class));
+			// Map the parameters values to the model
+			if (condition.has("parameters")) {
+				ScenarioExtraction.getModelParameters(condition.get("parameters"), modelCopy);
+			}
+
+			// Map the initials values to the model
+			if (condition.has("initials")) {
+				ScenarioExtraction.getModelInitials(condition.get("initials"), modelCopy);
 			}
 
 			// Fetch the dataset names
-			final List<String> datasetsNames = List.of();
+			final List<String> datasetsNames = new ArrayList<>(List.of());
 			props.datasetIds.forEach(datasetId -> {
 				final Optional<Dataset> dataset = datasetService.getAsset(datasetId, ASSUME_WRITE_PERMISSION_ON_BEHALF_OF_USER);
 				dataset.ifPresent(value -> datasetsNames.add(value.getName()));

From 0480fb380e4015af18f6aaccac2b063da82aefbf Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 15:28:04 -0400
Subject: [PATCH 15/19] Remove unused methods

---
 .../ModelConfigurationController.java         | 36 -------------------
 .../service/data/ProvenanceSearchService.java | 36 -------------------
 2 files changed, 72 deletions(-)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
index 5c6ee65c08..0f6ca3de91 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
@@ -159,42 +159,6 @@ public ResponseEntity<ModelConfiguration> getModelConfiguration(
 		}
 	}
 
-	/**
-	 * Gets all the Document and Dataset provenance from a model configuration
-	 *
-	 * @param id UUID of the model configuration
-	 * @return the list of asset ids and types
-	 */
-	@GetMapping("/{id}/extracted-from")
-	@Secured(Roles.USER)
-	@Operation(summary = "Gets all the Document and Dataset provenance from a model configuration")
-	@ApiResponses(
-		value = {
-			@ApiResponse(
-				responseCode = "200",
-				description = "Provenances found.",
-				content = @Content(array = @ArraySchema(schema = @Schema(implementation = Provenance.class)))
-			),
-			@ApiResponse(
-				responseCode = "503",
-				description = "There was an issue communicating with back-end services",
-				content = @Content
-			)
-		}
-	)
-	public ResponseEntity<Set<Provenance>> getExtractedFrom(@PathVariable("id") final UUID id) {
-		try {
-			final Set<Provenance> provenances = provenanceSearchService.modelConfigSource(id);
-			return ResponseEntity.ok(provenances);
-		} catch (final Exception e) {
-			log.error("Unable to get model0configuration extraction source from the neo4j db", e);
-			throw new ResponseStatusException(
-				org.springframework.http.HttpStatus.SERVICE_UNAVAILABLE,
-				messages.get("neo4j.service-unavailable")
-			);
-		}
-	}
-
 	/**
 	 * Create a configured model from a model config
 	 *
diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java
index 73cd16c382..d4cafaf9ed 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/data/ProvenanceSearchService.java
@@ -17,7 +17,6 @@
 import org.neo4j.driver.types.Node;
 import org.neo4j.driver.types.Relationship;
 import org.springframework.stereotype.Service;
-import software.uncharted.terarium.hmiserver.models.dataservice.provenance.Provenance;
 import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceEdge;
 import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceNode;
 import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceQueryParam;
@@ -97,41 +96,6 @@ public ProvenanceSearchResult concept(final ProvenanceQueryParam payload) {
 		}
 	}
 
-	/**
-	 * Get the documents and datasets used to create a model configuration
-	 *
-	 * @param id - Model configuration id.
-	 * @return Set<Provenance> - The Documents and Datasets used to create a model configuration.
-	 */
-	public Set<Provenance> modelConfigSource(final UUID id) {
-		final Set<Provenance> provenances = new HashSet<>();
-		try (final Session session = neo4jService.getSession()) {
-			final String query = String.format(
-				"MATCH (d:Document)<-[r:EXTRACTED_FROM]-(m:ModelConfiguration {id: '%s'}) RETURN d.id as id, 'DOCUMENT' as type " +
-				"UNION " +
-				"MATCH (ds:Dataset)<-[r:EXTRACTED_FROM]-(m:ModelConfiguration {id: '%s'}) RETURN ds.id as id, 'DATASET' as type",
-				id,
-				id
-			);
-
-			final Result response = session.run(query);
-			while (response.hasNext()) {
-				final var record = response.next();
-				final ProvenanceType recordType = record.get("type").asString().equals("DOCUMENT")
-					? ProvenanceType.DOCUMENT
-					: ProvenanceType.DATASET;
-				final Provenance provenance = new Provenance();
-				provenance.setLeft(id);
-				provenance.setLeftType(ProvenanceType.MODEL_CONFIGURATION);
-				provenance.setRight(UUID.fromString(record.get("id").asString()));
-				provenance.setRightType(recordType);
-				provenance.setRelationType(ProvenanceRelationType.EXTRACTED_FROM);
-				provenances.add(provenance);
-			}
-			return provenances;
-		}
-	}
-
 	/**
 	 * Identifies the document from which a model was extracted
 	 *

From 48736212fe8c42c05f765c7a5643f1f151471401 Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 15:29:43 -0400
Subject: [PATCH 16/19] Update ModelConfigurationController.java

---
 .../controller/dataservice/ModelConfigurationController.java  | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
index 0f6ca3de91..6918cd10b2 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelConfigurationController.java
@@ -9,7 +9,6 @@
 import java.io.IOException;
 import java.util.List;
 import java.util.Optional;
-import java.util.Set;
 import java.util.UUID;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
@@ -29,13 +28,11 @@
 import software.uncharted.terarium.hmiserver.models.dataservice.ResponseDeleted;
 import software.uncharted.terarium.hmiserver.models.dataservice.model.Model;
 import software.uncharted.terarium.hmiserver.models.dataservice.model.configurations.ModelConfiguration;
-import software.uncharted.terarium.hmiserver.models.dataservice.provenance.Provenance;
 import software.uncharted.terarium.hmiserver.security.Roles;
 import software.uncharted.terarium.hmiserver.service.CurrentUserService;
 import software.uncharted.terarium.hmiserver.service.data.ModelConfigurationService;
 import software.uncharted.terarium.hmiserver.service.data.ModelService;
 import software.uncharted.terarium.hmiserver.service.data.ProjectService;
-import software.uncharted.terarium.hmiserver.service.data.ProvenanceSearchService;
 import software.uncharted.terarium.hmiserver.utils.Messages;
 import software.uncharted.terarium.hmiserver.utils.rebac.Schema.Permission;
 
@@ -50,7 +47,6 @@ public class ModelConfigurationController {
 	final CurrentUserService currentUserService;
 	final Messages messages;
 	final ProjectService projectService;
-	final ProvenanceSearchService provenanceSearchService;
 
 	/**
 	 * Gets all model configurations (which are visible to this user)

From 9b4181b6c79d7069cbadafcc85ef28b189901af4 Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 15:30:58 -0400
Subject: [PATCH 17/19] Update ConfigureFromDatasetResponseHandler.java

---
 .../service/tasks/ConfigureFromDatasetResponseHandler.java      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
index 8330599bde..e19578a02a 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
@@ -118,7 +118,7 @@ public TaskResponse onSuccess(final TaskResponse resp) {
 				"This configuration was created from the dataset(s): " + source
 			);
 
-			// Update the source of the model-configuration with the Document name
+			// Update the source of the model-configuration with the datasets names
 			modelConfiguration.getInitialSemanticList().forEach(initial -> initial.setSource(source));
 			modelConfiguration.getParameterSemanticList().forEach(parameter -> parameter.setSource(source));
 

From 33fd00a8a679392e33eaa3bebfd3d94c5315e66e Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 15:33:44 -0400
Subject: [PATCH 18/19] Update ConfigureFromDatasetResponseHandler.java

---
 .../service/tasks/ConfigureFromDatasetResponseHandler.java      | 2 --
 1 file changed, 2 deletions(-)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
index e19578a02a..4e7d4a8fc4 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/service/tasks/ConfigureFromDatasetResponseHandler.java
@@ -90,8 +90,6 @@ public TaskResponse onSuccess(final TaskResponse resp) {
 			ScenarioExtraction.setNullDefaultModelParameters(modelCopy);
 
 			final JsonNode condition = configurations.getResponse().get("values");
-			final List<ModelParameter> modelParameters = ScenarioExtraction.getModelParameters(condition, modelCopy);
-			final List<Initial> modelInitials = ScenarioExtraction.getModelInitials(condition, modelCopy);
 
 			// Map the parameters values to the model
 			if (condition.has("parameters")) {

From 17fc01f2c8d3a4f40643b7892c358bfa6fbe693b Mon Sep 17 00:00:00 2001
From: Yohann Paris <github@yohannparis.com>
Date: Fri, 16 Aug 2024 15:37:58 -0400
Subject: [PATCH 19/19] oopsie, it's Friday evening.

---
 .../dataservice/model/configurations/InitialSemantic.java   | 6 +-----
 .../dataservice/model/configurations/ParameterSemantic.java | 6 +-----
 2 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/InitialSemantic.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/InitialSemantic.java
index 4b0db367c6..715477d6cf 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/InitialSemantic.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/InitialSemantic.java
@@ -47,11 +47,7 @@ public InitialSemantic clone() {
 
 	@Override
 	public void setSource(String source) {
-		if (this.getSource() != null) {
-			return;
-		}
-
-		if (this.expression != null || this.expressionMathml != null) {
+		if ((this.expression != null || this.expressionMathml != null) && this.getSource() != null) {
 			super.setSource(source);
 		}
 	}
diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/ParameterSemantic.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/ParameterSemantic.java
index 7e78eae76e..e406547d07 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/ParameterSemantic.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/configurations/ParameterSemantic.java
@@ -49,11 +49,7 @@ public ParameterSemantic clone() {
 
 	@Override
 	public void setSource(String source) {
-		if (this.getSource() != null) {
-			return;
-		}
-
-		if (!this.getDistribution().getParameters().isEmpty()) {
+		if (!this.getDistribution().getParameters().isEmpty() && this.getSource() != null) {
 			super.setSource(source);
 		}
 	}