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Rework Model, Dataset and Document models to use the same underlying dkg #5469

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Nov 12, 2024
Merged

Rework Model, Dataset and Document models to use the same underlying dkg #5469

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7aeca4a
Rework Model, Dataset and Document models to use the same underlying …
dvince2 Nov 12, 2024
0731f79
chore: update generated types
dvince2 Nov 12, 2024
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9 changes: 2 additions & 7 deletions packages/client/hmi-client/src/types/Types.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -115,15 +115,10 @@ export interface CsvColumnStats {
}

export interface Grounding extends TerariumEntity {
identifiers: Identifier[];
identifiers: DKG[];
context?: any;
}

export interface Identifier {
curie: string;
name: string;
}

export interface PresignedURL {
url: string;
method: string;
Expand Down Expand Up @@ -799,10 +794,10 @@ export interface ModelUnit {
}

export interface GroundedSemantic {
grounding?: ModelGrounding;
id: string;
name?: string;
description?: string;
grounding?: ModelGrounding;
}

export interface Properties {
Expand Down
4 changes: 2 additions & 2 deletions .../java/software/uncharted/terarium/hmiserver/controller/knowledge/KnowledgeController.java
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Expand Up @@ -46,7 +46,6 @@
import org.springframework.web.multipart.MultipartFile;
import org.springframework.web.server.ResponseStatusException;
import software.uncharted.terarium.hmiserver.models.dataservice.Grounding;
import software.uncharted.terarium.hmiserver.models.dataservice.Identifier;
import software.uncharted.terarium.hmiserver.models.dataservice.code.Code;
import software.uncharted.terarium.hmiserver.models.dataservice.code.CodeFile;
import software.uncharted.terarium.hmiserver.models.dataservice.dataset.Dataset;
Expand All @@ -59,6 +58,7 @@
import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceRelationType;
import software.uncharted.terarium.hmiserver.models.dataservice.provenance.ProvenanceType;
import software.uncharted.terarium.hmiserver.models.extractionservice.ExtractionResponse;
import software.uncharted.terarium.hmiserver.models.mira.DKG;
import software.uncharted.terarium.hmiserver.models.task.TaskRequest;
import software.uncharted.terarium.hmiserver.models.task.TaskRequest.TaskType;
import software.uncharted.terarium.hmiserver.models.task.TaskResponse;
Expand Down Expand Up @@ -679,7 +679,7 @@ public ResponseEntity<Dataset> postProfileDataset(
if (groundings.getIdentifiers() == null) {
groundings.setIdentifiers(new ArrayList<>());
}
groundings.getIdentifiers().add(new Identifier(g.get(0).asText(), g.get(1).asText()));
groundings.getIdentifiers().add(new DKG(g.get(0).asText(), g.get(1).asText(), null));
}

// remove groundings from annotation object
Expand Down
3 changes: 2 additions & 1 deletion ...ver/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/Grounding.java
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Expand Up @@ -14,6 +14,7 @@
import software.uncharted.terarium.hmiserver.annotations.TSModel;
import software.uncharted.terarium.hmiserver.annotations.TSOptional;
import software.uncharted.terarium.hmiserver.models.TerariumEntity;
import software.uncharted.terarium.hmiserver.models.mira.DKG;

/** Represents a grounding document from TDS */
@Data
Expand All @@ -29,7 +30,7 @@ public class Grounding extends TerariumEntity {
/** Ontological identifier per DKG */
@Type(JsonType.class)
@Column(columnDefinition = "json")
private List<Identifier> identifiers;
private List<DKG> identifiers;

/** (Optional) Additional context that informs the grounding */
@TSOptional
Expand Down
11 changes: 0 additions & 11 deletions ...er/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/Identifier.java
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This file was deleted.

3 changes: 3 additions & 0 deletions packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/mira/DKG.java
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Expand Up @@ -2,14 +2,17 @@

import com.fasterxml.jackson.annotation.JsonAlias;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import lombok.AllArgsConstructor;
import lombok.Data;
import lombok.RequiredArgsConstructor;
import lombok.experimental.Accessors;
import software.uncharted.terarium.hmiserver.annotations.TSModel;

@Data
@Accessors(chain = true)
@JsonIgnoreProperties(ignoreUnknown = true)
@TSModel
@AllArgsConstructor
public class DKG {

public static final String ID = "id:ID";
Expand Down
16 changes: 8 additions & 8 deletions ...src/test/java/software/uncharted/terarium/hmiserver/service/data/DatasetServiceTests.java
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Expand Up @@ -16,10 +16,10 @@
import software.uncharted.terarium.hmiserver.TerariumApplicationTests;
import software.uncharted.terarium.hmiserver.configuration.MockUser;
import software.uncharted.terarium.hmiserver.models.dataservice.Grounding;
import software.uncharted.terarium.hmiserver.models.dataservice.Identifier;
import software.uncharted.terarium.hmiserver.models.dataservice.dataset.Dataset;
import software.uncharted.terarium.hmiserver.models.dataservice.dataset.DatasetColumn;
import software.uncharted.terarium.hmiserver.models.dataservice.project.Project;
import software.uncharted.terarium.hmiserver.models.mira.DKG;

@Slf4j
public class DatasetServiceTests extends TerariumApplicationTests {
Expand Down Expand Up @@ -60,7 +60,7 @@ static Grounding createGrounding(final String key) {
final Grounding grounding = new Grounding();
grounding.setContext(mapper.createObjectNode().put("hello", "world-" + key).put("foo", "bar-" + key));
grounding.setIdentifiers(new ArrayList<>());
grounding.getIdentifiers().add(new Identifier("curie", "maria"));
grounding.getIdentifiers().add(new DKG("curie", "maria", null));
return grounding;
}

Expand Down Expand Up @@ -116,8 +116,8 @@ public void testItCanCreateDataset() throws Exception {
Assertions.assertNotNull(col.getGrounding().getCreatedOn());
Assertions.assertNotNull(col.getGrounding().getIdentifiers());
Assertions.assertEquals(col.getGrounding().getIdentifiers().size(), 1);
Assertions.assertNotNull(col.getGrounding().getIdentifiers().get(0).curie());
Assertions.assertNotNull(col.getGrounding().getIdentifiers().get(0).name());
Assertions.assertNotNull(col.getGrounding().getIdentifiers().get(0).getCurie());
Assertions.assertNotNull(col.getGrounding().getIdentifiers().get(0).getName());
Assertions.assertNotNull(col.getGrounding().getContext());
Assertions.assertEquals(col.getGrounding().getContext().size(), 2);
}
Expand All @@ -126,8 +126,8 @@ public void testItCanCreateDataset() throws Exception {
Assertions.assertNotNull(after.getGrounding().getId());
Assertions.assertNotNull(after.getGrounding().getCreatedOn());
Assertions.assertNotNull(after.getGrounding().getIdentifiers());
Assertions.assertNotNull(after.getGrounding().getIdentifiers().get(0).curie());
Assertions.assertNotNull(after.getGrounding().getIdentifiers().get(0).name());
Assertions.assertNotNull(after.getGrounding().getIdentifiers().get(0).getCurie());
Assertions.assertNotNull(after.getGrounding().getIdentifiers().get(0).getName());
Assertions.assertNotNull(after.getGrounding().getContext());
Assertions.assertEquals(after.getGrounding().getContext().size(), 2);
}
Expand Down Expand Up @@ -169,8 +169,8 @@ public void testItCanCreateDatasetAndAddColumnsLater() throws Exception {
Assertions.assertNotNull(col.getGrounding().getCreatedOn());
Assertions.assertNotNull(col.getGrounding().getIdentifiers());
Assertions.assertEquals(col.getGrounding().getIdentifiers().size(), 1);
Assertions.assertNotNull(col.getGrounding().getIdentifiers().get(0).curie());
Assertions.assertNotNull(col.getGrounding().getIdentifiers().get(0).name());
Assertions.assertNotNull(col.getGrounding().getIdentifiers().get(0).getCurie());
Assertions.assertNotNull(col.getGrounding().getIdentifiers().get(0).getName());
Assertions.assertNotNull(col.getGrounding().getContext());
Assertions.assertEquals(col.getGrounding().getContext().size(), 2);
}
Expand Down
8 changes: 4 additions & 4 deletions ...rc/test/java/software/uncharted/terarium/hmiserver/service/data/DocumentServiceTests.java
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Expand Up @@ -18,11 +18,11 @@
import software.uncharted.terarium.hmiserver.TerariumApplicationTests;
import software.uncharted.terarium.hmiserver.configuration.MockUser;
import software.uncharted.terarium.hmiserver.models.dataservice.Grounding;
import software.uncharted.terarium.hmiserver.models.dataservice.Identifier;
import software.uncharted.terarium.hmiserver.models.dataservice.document.DocumentAsset;
import software.uncharted.terarium.hmiserver.models.dataservice.document.DocumentExtraction;
import software.uncharted.terarium.hmiserver.models.dataservice.document.ExtractionAssetType;
import software.uncharted.terarium.hmiserver.models.dataservice.project.Project;
import software.uncharted.terarium.hmiserver.models.mira.DKG;

@Slf4j
public class DocumentServiceTests extends TerariumApplicationTests {
Expand Down Expand Up @@ -63,7 +63,7 @@ static Grounding createGrounding(final String key) {
final Grounding grounding = new Grounding();
grounding.setContext(mapper.createObjectNode().put("hello", "world-" + key).put("foo", "bar-" + key));
grounding.setIdentifiers(new ArrayList<>());
grounding.getIdentifiers().add(new Identifier("curie", "maria"));
grounding.getIdentifiers().add(new DKG("curie", "maria", null));
return grounding;
}

Expand Down Expand Up @@ -106,8 +106,8 @@ public void testItCanCreateDocument() throws Exception {
Assertions.assertNotNull(after.getGrounding().getId());
Assertions.assertNotNull(after.getGrounding().getCreatedOn());
Assertions.assertNotNull(after.getGrounding().getIdentifiers());
Assertions.assertNotNull(after.getGrounding().getIdentifiers().get(0).curie());
Assertions.assertNotNull(after.getGrounding().getIdentifiers().get(0).name());
Assertions.assertNotNull(after.getGrounding().getIdentifiers().get(0).getCurie());
Assertions.assertNotNull(after.getGrounding().getIdentifiers().get(0).getName());
Assertions.assertNotNull(after.getGrounding().getContext());
Assertions.assertEquals(after.getGrounding().getContext().size(), 2);
}
Expand Down
4 changes: 2 additions & 2 deletions ...va/software/uncharted/terarium/hmiserver/service/data/TerariumAssetCloneServiceTests.java
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Expand Up @@ -18,7 +18,6 @@
import software.uncharted.terarium.hmiserver.models.TerariumAsset;
import software.uncharted.terarium.hmiserver.models.dataservice.AssetType;
import software.uncharted.terarium.hmiserver.models.dataservice.Grounding;
import software.uncharted.terarium.hmiserver.models.dataservice.Identifier;
import software.uncharted.terarium.hmiserver.models.dataservice.document.DocumentAsset;
import software.uncharted.terarium.hmiserver.models.dataservice.document.DocumentExtraction;
import software.uncharted.terarium.hmiserver.models.dataservice.document.ExtractionAssetType;
Expand All @@ -29,6 +28,7 @@
import software.uncharted.terarium.hmiserver.models.dataservice.workflow.Workflow;
import software.uncharted.terarium.hmiserver.models.dataservice.workflow.WorkflowEdge;
import software.uncharted.terarium.hmiserver.models.dataservice.workflow.WorkflowNode;
import software.uncharted.terarium.hmiserver.models.mira.DKG;
import software.uncharted.terarium.hmiserver.service.TerariumAssetCloneService;

public class TerariumAssetCloneServiceTests extends TerariumApplicationTests {
Expand Down Expand Up @@ -74,7 +74,7 @@ static Grounding createGrounding(final String key) {
final Grounding grounding = new Grounding();
grounding.setContext(objectMapper.createObjectNode().put("hello", "world-" + key).put("foo", "bar-" + key));
grounding.setIdentifiers(new ArrayList<>());
grounding.getIdentifiers().add(new Identifier("curie", "maria"));
grounding.getIdentifiers().add(new DKG("curie", "maria", null));
return grounding;
}

Expand Down