From 4bbbde7a67a8c7170b8baf4e313eec542061ab0a Mon Sep 17 00:00:00 2001
From: Martin Weise <martin.weise@tuwien.ac.at>
Date: Tue, 27 Aug 2024 07:39:12 +0200
Subject: [PATCH] WIP
---
dbrepo-metadata-db/1_setup-schema.sql | 12 +-
.../table/columns/ColumnCreateDto.java | 6 +
.../concepts/ColumnSemanticsUpdateDto.java | 6 +
.../java/at/tuwien/mapper/MetadataMapper.java | 6 +
.../at/tuwien/endpoints/OntologyEndpoint.java | 71 +-------
.../at/tuwien/endpoints/TableEndpoint.java | 94 +---------
.../endpoints/OntologyEndpointUnitTest.java | 109 ------------
.../endpoints/TableEndpointUnitTest.java | 91 ----------
.../tuwien/mvc/PrometheusEndpointMvcTest.java | 15 --
.../tuwien/service/EntityServiceUnitTest.java | 163 -----------------
.../java/at/tuwien/service/EntityService.java | 64 -------
.../service/impl/EntityServiceImpl.java | 167 ------------------
.../tuwien/service/impl/TableServiceImpl.java | 53 ++++--
dbrepo-ui/components/table/TableSchema.vue | 14 +-
dbrepo-ui/composables/table-service.ts | 23 +--
dbrepo-ui/dto/index.ts | 11 ++
16 files changed, 88 insertions(+), 817 deletions(-)
delete mode 100644 dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/service/EntityServiceUnitTest.java
delete mode 100644 dbrepo-metadata-service/services/src/main/java/at/tuwien/service/EntityService.java
delete mode 100644 dbrepo-metadata-service/services/src/main/java/at/tuwien/service/impl/EntityServiceImpl.java
diff --git a/dbrepo-metadata-db/1_setup-schema.sql b/dbrepo-metadata-db/1_setup-schema.sql
index 62dc5c3095..9213b8ea88 100644
--- a/dbrepo-metadata-db/1_setup-schema.sql
+++ b/dbrepo-metadata-db/1_setup-schema.sql
@@ -543,7 +543,7 @@ VALUES (1, '%Y-%c-%d %H:%i:%S.%f', 'yyyy-MM-dd HH:mm:ss.SSSSSS', '2022-01-30 13:
(1, '%d.%c.%Y', 'dd.MM.yyyy', '30.01.2022', false);
INSERT INTO `mdb_ontologies` (prefix, uri, uri_pattern, sparql_endpoint, rdf_path)
-VALUES ('om', 'http://www.ontology-of-units-of-measure.org/resource/om-2/',
+VALUES ('om2', 'http://www.ontology-of-units-of-measure.org/resource/om-2/',
'http://www.ontology-of-units-of-measure.org/resource/om-2/.*', null, 'rdf/om-2.0.rdf'),
('wd', 'http://www.wikidata.org/', 'http://www.wikidata.org/entity/.*', 'https://query.wikidata.org/sparql',
null),
@@ -557,5 +557,13 @@ VALUES ('om', 'http://www.ontology-of-units-of-measure.org/resource/om-2/',
('rdfs', 'http://www.w3.org/2000/01/rdf-schema#', null, null, null),
('owl', 'http://www.w3.org/2002/07/owl#', null, null, null),
('prov', 'http://www.w3.org/ns/prov#', null, null, null),
- ('db', 'http://dbpedia.org', 'http://dbpedia.org/ontology/.*', 'http://dbpedia.org/sparql', null);
+ ('db', 'http://dbpedia.org', 'http://dbpedia.org/ontology/.*', 'http://dbpedia.org/sparql', null),
+ ('aq', 'http://vocab.linkeddata.es/datosabiertos/def/medio-ambiente/calidad-aire', 'http://vocab.linkeddata.es/datosabiertos/def/medio-ambiente/calidad-aire/*', null, null),
+ ('building', 'https://www.auto.tuwien.ac.at/downloads/thinkhome/ontology/BuildingOntology.owl', 'https://www.auto.tuwien.ac.at/downloads/thinkhome/ontology/BuildingOntology.owl/*', null, null),
+ ('car', 'https://spec.edmcouncil.org/auto/ontology/VC/VehicleCore/', 'https://spec.edmcouncil.org/auto/ontology/VC/VehicleCore/*', null, null),
+ ('fff', 'http://sbmi.uth.edu/ontology/offf', 'http://sbmi.uth.edu/ontology/offf/*', null, null),
+ ('wq', 'http://purl.org/nemo/doce#/2022-02-23', 'http://purl.org/nemo/doce#/2022-02-23/*', null, null),
+ ('weather', 'https://www.auto.tuwien.ac.at/downloads/thinkhome/ontology/WeatherOntology.owl', 'https://www.auto.tuwien.ac.at/downloads/thinkhome/ontology/WeatherOntology.owl/*', null, null),
+ ('qudt', 'http://qudt.org/2.1/vocab/quantitykind', 'http://qudt.org/2.1/vocab/quantitykind/*', null, null),
+ ('ucum', 'http://elite.polito.it/ontologies/ucum-instances.owl', 'http://elite.polito.it/ontologies/ucum-instances.owl/*', null, null);
COMMIT;
diff --git a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/database/table/columns/ColumnCreateDto.java b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/database/table/columns/ColumnCreateDto.java
index 37aa493020..03e224bc31 100644
--- a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/database/table/columns/ColumnCreateDto.java
+++ b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/database/table/columns/ColumnCreateDto.java
@@ -49,9 +49,15 @@ public class ColumnCreateDto {
@JsonProperty("concept_uri")
private String conceptUri;
+ @JsonProperty("concept_label")
+ private String conceptLabel;
+
@JsonProperty("unit_uri")
private String unitUri;
+ @JsonProperty("unit_label")
+ private String unitLabel;
+
@Schema(description = "date format id")
private Long dfid;
diff --git a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ColumnSemanticsUpdateDto.java b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ColumnSemanticsUpdateDto.java
index 77a38f70b4..4d0533e11a 100644
--- a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ColumnSemanticsUpdateDto.java
+++ b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ColumnSemanticsUpdateDto.java
@@ -16,6 +16,12 @@ public class ColumnSemanticsUpdateDto {
@JsonProperty("concept_uri")
private String conceptUri;
+ @JsonProperty("concept_label")
+ private String conceptLabel;
+
@JsonProperty("unit_uri")
private String unitUri;
+
+ @JsonProperty("unit_label")
+ private String unitLabel;
}
diff --git a/dbrepo-metadata-service/repositories/src/main/java/at/tuwien/mapper/MetadataMapper.java b/dbrepo-metadata-service/repositories/src/main/java/at/tuwien/mapper/MetadataMapper.java
index 557d1e49ab..ff5b4f5361 100644
--- a/dbrepo-metadata-service/repositories/src/main/java/at/tuwien/mapper/MetadataMapper.java
+++ b/dbrepo-metadata-service/repositories/src/main/java/at/tuwien/mapper/MetadataMapper.java
@@ -455,8 +455,14 @@ public interface MetadataMapper {
TableColumnUnit unitSaveDtoToTableColumnUnit(UnitSaveDto data);
+ @Mappings({
+ @Mapping(target = "name", source = "label"),
+ })
TableColumnUnit entityDtoToTableColumnUnit(EntityDto data);
+ @Mappings({
+ @Mapping(target = "name", source = "label"),
+ })
TableColumnConcept entityDtoToTableColumnConcept(EntityDto data);
TableColumnConcept conceptSaveDtoToTableColumnConcept(ConceptSaveDto data);
diff --git a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/OntologyEndpoint.java b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/OntologyEndpoint.java
index cd17c7ac0b..ac14066b41 100644
--- a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/OntologyEndpoint.java
+++ b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/OntologyEndpoint.java
@@ -5,8 +5,6 @@ import at.tuwien.api.semantics.*;
import at.tuwien.entities.semantics.Ontology;
import at.tuwien.exception.*;
import at.tuwien.mapper.MetadataMapper;
-import at.tuwien.mapper.SparqlMapper;
-import at.tuwien.service.EntityService;
import at.tuwien.service.OntologyService;
import io.micrometer.observation.annotation.Observed;
import io.swagger.v3.oas.annotations.Operation;
@@ -34,14 +32,11 @@ import java.util.List;
@RequestMapping(path = "/api/ontology")
public class OntologyEndpoint {
- private final EntityService entityService;
private final MetadataMapper metadataMapper;
private final OntologyService ontologyService;
@Autowired
- public OntologyEndpoint(EntityService entityService, MetadataMapper metadataMapper,
- OntologyService ontologyService) {
- this.entityService = entityService;
+ public OntologyEndpoint(MetadataMapper metadataMapper, OntologyService ontologyService) {
this.metadataMapper = metadataMapper;
this.ontologyService = ontologyService;
}
@@ -164,68 +159,4 @@ public class OntologyEndpoint {
.build();
}
- @GetMapping("/{ontologyId}/entity")
- @PreAuthorize("hasAuthority('execute-semantic-query')")
- @Observed(name = "dbrepo_ontologies_entities_find")
- @Operation(summary = "Find entities",
- description = "Finds semantic entities by label or uri in an ontology with id. Requires role `execute-semantic-query`.",
- security = {@SecurityRequirement(name = "bearerAuth"), @SecurityRequirement(name = "basicAuth")})
- @ApiResponses(value = {
- @ApiResponse(responseCode = "200",
- description = "Found entities",
- content = {@Content(
- mediaType = "application/json",
- array = @ArraySchema(schema = @Schema(implementation = EntityDto.class)))}),
- @ApiResponse(responseCode = "400",
- description = "Filter params are invalid",
- content = {@Content(
- mediaType = "application/json",
- schema = @Schema(implementation = ApiErrorDto.class))}),
- @ApiResponse(responseCode = "404",
- description = "Could not find ontology",
- content = {@Content(
- mediaType = "application/json",
- schema = @Schema(implementation = ApiErrorDto.class))}),
- @ApiResponse(responseCode = "417",
- description = "Generated query or uri is malformed",
- content = {@Content(
- mediaType = "application/json",
- schema = @Schema(implementation = ApiErrorDto.class))}),
- @ApiResponse(responseCode = "422",
- description = "Ontology does not have rdf or sparql endpoint",
- content = {@Content(
- mediaType = "application/json",
- schema = @Schema(implementation = ApiErrorDto.class))}),
- })
- public ResponseEntity<List<EntityDto>> find(@NotNull @PathVariable("ontologyId") Long id,
- @RequestParam(name = "label", required = false) String label,
- @RequestParam(name = "uri", required = false) String uri)
- throws OntologyNotFoundException, UriMalformedException, FilterBadRequestException, MalformedException {
- log.debug("endpoint find entities by uri, id={}, label={}, uri={}", id, label, uri);
- final Ontology ontology = ontologyService.find(id);
- /* check */
- if ((label != null && uri != null) || (label == null && uri == null)) {
- log.error("Failed to find entities: either label or uri must be defined");
- throw new FilterBadRequestException("Failed to find entities: either label or uri must be defined");
- }
- if (uri != null && !uri.startsWith(ontology.getUri())) {
- log.error("Failed to find entities: uri {} does not start with expected ontology uri {}", uri, ontology.getUri());
- throw new UriMalformedException("Failed to find entity: uri " + uri + " does not start with expected ontology uri " + ontology.getUri());
- }
- if (ontology.getSparqlEndpoint() == null) {
- log.error("Failed to find SPARQL endpoint for ontology with id {}", ontology.getId());
- throw new OntologyNotFoundException("Failed to find SPARQL endpoint for ontology with id " + ontology.getId());
- }
- /* get */
- final List<EntityDto> dtos;
- if (uri != null) {
- dtos = entityService.findByUri(uri);
- return ResponseEntity.ok()
- .body(dtos);
- }
- dtos = entityService.findByLabel(ontology, label);
- return ResponseEntity.ok()
- .body(dtos);
- }
-
}
diff --git a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
index 4fb8240b1d..9b4fb753a3 100644
--- a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
+++ b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
@@ -8,8 +8,6 @@ import at.tuwien.api.database.table.columns.ColumnDto;
import at.tuwien.api.database.table.columns.ColumnTypeDto;
import at.tuwien.api.database.table.columns.concepts.ColumnSemanticsUpdateDto;
import at.tuwien.api.error.ApiErrorDto;
-import at.tuwien.api.semantics.EntityDto;
-import at.tuwien.api.semantics.TableColumnEntityDto;
import at.tuwien.entities.database.Database;
import at.tuwien.entities.database.table.Table;
import at.tuwien.entities.database.table.columns.TableColumn;
@@ -50,18 +48,15 @@ public class TableEndpoint {
private final UserService userService;
private final TableService tableService;
- private final EntityService entityService;
private final MetadataMapper metadataMapper;
private final DatabaseService databaseService;
private final EndpointValidator endpointValidator;
@Autowired
- public TableEndpoint(UserService userService, TableService tableService, EntityService entityService,
- MetadataMapper metadataMapper, DatabaseService databaseService,
- EndpointValidator endpointValidator) {
+ public TableEndpoint(UserService userService, TableService tableService, MetadataMapper metadataMapper,
+ DatabaseService databaseService, EndpointValidator endpointValidator) {
this.userService = userService;
this.tableService = tableService;
- this.entityService = entityService;
this.metadataMapper = metadataMapper;
this.databaseService = databaseService;
this.endpointValidator = endpointValidator;
@@ -105,50 +100,6 @@ public class TableEndpoint {
return ResponseEntity.ok(dto);
}
- @GetMapping("/{tableId}/suggest")
- @Transactional(readOnly = true)
- @PreAuthorize("hasAuthority('table-semantic-analyse')")
- @Observed(name = "dbrepo_semantic_table_analyse")
- @Operation(summary = "Suggest semantics",
- description = "Suggests semantic concepts for a table. Requires role `table-semantic-analyse`.",
- security = {@SecurityRequirement(name = "bearerAuth"), @SecurityRequirement(name = "basicAuth")})
- @ApiResponses(value = {
- @ApiResponse(responseCode = "200",
- description = "Suggested table semantics successfully",
- content = {@Content(
- mediaType = "application/json",
- array = @ArraySchema(schema = @Schema(implementation = EntityDto.class)))}),
- @ApiResponse(responseCode = "400",
- description = "Failed to parse statistic in search service",
- content = {@Content(
- mediaType = "application/json",
- schema = @Schema(implementation = ApiErrorDto.class))}),
- @ApiResponse(responseCode = "404",
- description = "Failed to find database/table in metadata database",
- content = {@Content(
- mediaType = "application/json",
- schema = @Schema(implementation = ApiErrorDto.class))}),
- @ApiResponse(responseCode = "417",
- description = "Generated query is malformed",
- content = {@Content(
- mediaType = "application/json",
- schema = @Schema(implementation = ApiErrorDto.class))}),
- @ApiResponse(responseCode = "422",
- description = "Ontology does not have rdf or sparql endpoint",
- content = {@Content(
- mediaType = "application/json",
- schema = @Schema(implementation = ApiErrorDto.class))}),
- })
- public ResponseEntity<List<EntityDto>> analyseTable(@NotNull @PathVariable("databaseId") Long databaseId,
- @NotNull @PathVariable("tableId") Long tableId)
- throws MalformedException, TableNotFoundException, DatabaseNotFoundException {
- log.debug("endpoint analyse table semantics, databaseId={}, tableId={}", databaseId, tableId);
- final Table table = tableService.findById(databaseId, tableId);
- final List<EntityDto> dtos = entityService.suggestByTable(table);
- return ResponseEntity.ok()
- .body(dtos);
- }
-
@PutMapping("/{tableId}")
@Transactional
@PreAuthorize("hasAuthority('update-table-statistic')")
@@ -254,47 +205,6 @@ public class TableEndpoint {
.body(columnDto);
}
- @GetMapping("/{tableId}/column/{columnId}/suggest")
- @Transactional(readOnly = true)
- @PreAuthorize("hasAuthority('table-semantic-analyse')")
- @Observed(name = "dbrepo_semantic_column_analyse")
- @Operation(summary = "Suggest semantics",
- description = "Suggests column semantics. Requires role `table-semantic-analyse`.",
- security = {@SecurityRequirement(name = "bearerAuth"), @SecurityRequirement(name = "basicAuth")})
- @ApiResponses(value = {
- @ApiResponse(responseCode = "200",
- description = "Suggested table column semantics successfully",
- content = {@Content(
- mediaType = "application/json",
- array = @ArraySchema(schema = @Schema(implementation = TableColumnEntityDto.class)))}),
- @ApiResponse(responseCode = "400",
- description = "Generated query is malformed",
- content = {@Content(
- mediaType = "application/json",
- schema = @Schema(implementation = ApiErrorDto.class))}),
- @ApiResponse(responseCode = "404",
- description = "Failed to find database/table in metadata database",
- content = {@Content(
- mediaType = "application/json",
- schema = @Schema(implementation = ApiErrorDto.class))}),
- @ApiResponse(responseCode = "422",
- description = "Ontology does not have rdf or sparql endpoint",
- content = {@Content(
- mediaType = "application/json",
- schema = @Schema(implementation = ApiErrorDto.class))}),
- })
- public ResponseEntity<List<TableColumnEntityDto>> analyseTableColumn(@NotNull @PathVariable("databaseId") Long databaseId,
- @NotNull @PathVariable("tableId") Long tableId,
- @NotNull @PathVariable("columnId") Long columnId)
- throws MalformedException, TableNotFoundException, DatabaseNotFoundException {
- log.debug("endpoint analyse table column semantics, databaseId={}, tableId={}, columnId={}", databaseId, tableId, columnId);
- final Table table = tableService.findById(databaseId, tableId);
- TableColumn column = tableService.findColumnById(table, columnId);
- final List<TableColumnEntityDto> dtos = entityService.suggestByColumn(column);
- return ResponseEntity.ok()
- .body(dtos);
- }
-
@PostMapping
@Transactional(rollbackFor = {Exception.class})
@PreAuthorize("hasAuthority('create-table')")
diff --git a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/endpoints/OntologyEndpointUnitTest.java b/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/endpoints/OntologyEndpointUnitTest.java
index fc20a0b9e3..297c21a386 100644
--- a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/endpoints/OntologyEndpointUnitTest.java
+++ b/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/endpoints/OntologyEndpointUnitTest.java
@@ -5,7 +5,6 @@ import at.tuwien.api.semantics.*;
import at.tuwien.entities.semantics.Ontology;
import at.tuwien.entities.user.User;
import at.tuwien.exception.*;
-import at.tuwien.service.EntityService;
import at.tuwien.service.OntologyService;
import at.tuwien.service.UserService;
import lombok.extern.log4j.Log4j2;
@@ -37,9 +36,6 @@ public class OntologyEndpointUnitTest extends AbstractUnitTest {
@MockBean
private OntologyService ontologyService;
- @MockBean
- private EntityService entityService;
-
@MockBean
private UserService userService;
@@ -177,78 +173,6 @@ public class OntologyEndpointUnitTest extends AbstractUnitTest {
delete_generic(ONTOLOGY_1_ID, ONTOLOGY_1);
}
- @Test
- @WithAnonymousUser
- public void find_anonymous_fails() {
-
- /* test */
- assertThrows(org.springframework.security.access.AccessDeniedException.class, () -> {
- find_generic(ONTOLOGY_2_ID, "Apache Jena", null, ONTOLOGY_2, null);
- });
- }
-
- @Test
- @WithMockUser(username = USER_4_USERNAME, authorities = {})
- public void find_noRole_fails() {
-
- /* test */
- assertThrows(org.springframework.security.access.AccessDeniedException.class, () -> {
- find_generic(ONTOLOGY_2_ID, "Apache Jena", null, ONTOLOGY_2, null);
- });
- }
-
- @Test
- @WithMockUser(username = USER_1_USERNAME, authorities = {"execute-semantic-query"})
- public void find_hasRoleInvalidParams_succeeds() {
-
- /* test */
- assertThrows(FilterBadRequestException.class, () -> {
- find_generic(ONTOLOGY_2_ID, "Apache Jena", "http://www.wikidata.org/entity/Q1686799", ONTOLOGY_2, null);
- });
- }
-
- @Test
- @WithMockUser(username = USER_1_USERNAME, authorities = {"execute-semantic-query"})
- public void find_hasRoleNotOntologyUri_succeeds() {
-
- /* test */
- assertThrows(UriMalformedException.class, () -> {
- find_generic(ONTOLOGY_2_ID, null, "https://wikidata.org/entity/Q1686799", ONTOLOGY_2, null);
- });
- }
-
- @Test
- @WithMockUser(username = USER_1_USERNAME, authorities = {"execute-semantic-query"})
- public void find_hasRoleLabel_succeeds() throws MalformedException, UriMalformedException, OntologyNotFoundException,
- FilterBadRequestException {
- final EntityDto entityDto = EntityDto.builder()
- .label("Apache Jena")
- .uri("http://www.wikidata.org/entity/Q1686799")
- .build();
-
- /* test */
- final List<EntityDto> response = find_generic(ONTOLOGY_2_ID, "Apache Jena", null, ONTOLOGY_2, entityDto);
- final EntityDto entity0 = response.get(0);
- assertEquals("Apache Jena", entity0.getLabel());
- assertEquals("http://www.wikidata.org/entity/Q1686799", entity0.getUri());
- }
-
- @Test
- @WithMockUser(username = USER_1_USERNAME, authorities = {"execute-semantic-query"})
- public void find_hasRoleUri_succeeds() throws MalformedException, UriMalformedException, OntologyNotFoundException,
- FilterBadRequestException {
- final EntityDto entityDto = EntityDto.builder()
- .label("Apache Jena")
- .uri("http://www.wikidata.org/entity/Q1686799")
- .build();
-
- /* test */
- final List<EntityDto> response = find_generic(ONTOLOGY_2_ID, null, "http://www.wikidata.org/entity/Q1686799", ONTOLOGY_2, entityDto);
- final EntityDto entity0 = response.get(0);
- assertEquals("Apache Jena", entity0.getLabel());
- assertEquals("http://www.wikidata.org/entity/Q1686799", entity0.getUri());
- }
-
/* ################################################################################################### */
/* ## GENERIC TEST CASES ## */
/* ################################################################################################### */
@@ -347,37 +271,4 @@ public class OntologyEndpointUnitTest extends AbstractUnitTest {
final ResponseEntity<?> response = ontologyEndpoint.delete(ontologyId);
assertEquals(HttpStatus.ACCEPTED, response.getStatusCode());
}
-
- public List<EntityDto> find_generic(Long ontologyId, String label, String uri, Ontology ontology,
- EntityDto entityDto) throws MalformedException, UriMalformedException,
- FilterBadRequestException, OntologyNotFoundException {
-
- /* mock */
- if (ontology != null) {
- when(ontologyService.find(ontologyId))
- .thenReturn(ontology);
- } else {
- doThrow(OntologyNotFoundException.class)
- .when(ontologyService)
- .find(ontologyId);
- }
- if (entityDto != null) {
- when(entityService.findByLabel(ontology, label))
- .thenReturn(List.of(entityDto));
- when(entityService.findByUri(uri))
- .thenReturn(List.of(entityDto));
- } else {
- when(entityService.findByLabel(ontology, label))
- .thenReturn(List.of());
- when(entityService.findByUri(uri))
- .thenReturn(List.of());
- }
-
- /* test */
- final ResponseEntity<List<EntityDto>> response = ontologyEndpoint.find(ontologyId, label, uri);
- assertEquals(HttpStatus.OK, response.getStatusCode());
- final List<EntityDto> body = response.getBody();
- assertNotNull(body);
- return body;
- }
}
diff --git a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/endpoints/TableEndpointUnitTest.java b/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/endpoints/TableEndpointUnitTest.java
index 154ebda86c..2a9b4ec382 100644
--- a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/endpoints/TableEndpointUnitTest.java
+++ b/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/endpoints/TableEndpointUnitTest.java
@@ -8,8 +8,6 @@ import at.tuwien.api.database.table.columns.ColumnCreateDto;
import at.tuwien.api.database.table.columns.ColumnDto;
import at.tuwien.api.database.table.columns.ColumnTypeDto;
import at.tuwien.api.database.table.columns.concepts.ColumnSemanticsUpdateDto;
-import at.tuwien.api.semantics.EntityDto;
-import at.tuwien.api.semantics.TableColumnEntityDto;
import at.tuwien.entities.database.Database;
import at.tuwien.entities.database.DatabaseAccess;
import at.tuwien.entities.database.table.Table;
@@ -58,9 +56,6 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
@MockBean
private UserService userService;
- @MockBean
- private EntityService entityService;
-
@MockBean
private BrokerService messageQueueService;
@@ -395,64 +390,6 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
generic_findById(DATABASE_3_ID, DATABASE_3, TABLE_8_ID, TABLE_8, USER_1_PRINCIPAL, USER_1, null);
}
- @Test
- @WithAnonymousUser
- public void analyseTable_anonymous_fails() {
-
- /* test */
- assertThrows(org.springframework.security.access.AccessDeniedException.class, () -> {
- analyseTable_generic(DATABASE_1_ID, TABLE_1_ID, TABLE_1);
- });
- }
-
- @Test
- @WithMockUser(username = USER_4_USERNAME)
- public void findAll_noRole_fails() {
-
- /* test */
- assertThrows(org.springframework.security.access.AccessDeniedException.class, () -> {
- analyseTable_generic(DATABASE_1_ID, TABLE_1_ID, TABLE_1);
- });
- }
-
- @Test
- @WithMockUser(username = USER_1_USERNAME, authorities = {"table-semantic-analyse"})
- public void findAll_hasRole_succeeds() throws MalformedException, TableNotFoundException,
- DatabaseNotFoundException {
-
- /* test */
- analyseTable_generic(DATABASE_1_ID, TABLE_1_ID, TABLE_1);
- }
-
- @Test
- @WithAnonymousUser
- public void analyseTableColumn_anonymous_fails() {
-
- /* test */
- assertThrows(org.springframework.security.access.AccessDeniedException.class, () -> {
- analyseTableColumn_generic(DATABASE_1_ID, TABLE_1_ID, TABLE_1_COLUMNS.get(0).getId(), TABLE_1_COLUMNS.get(0));
- });
- }
-
- @Test
- @WithMockUser(username = USER_4_USERNAME)
- public void analyseTableColumn_noRole_fails() {
-
- /* test */
- assertThrows(org.springframework.security.access.AccessDeniedException.class, () -> {
- analyseTableColumn_generic(DATABASE_1_ID, TABLE_1_ID, TABLE_1_COLUMNS.get(0).getId(), TABLE_1_COLUMNS.get(0));
- });
- }
-
- @Test
- @WithMockUser(username = USER_1_USERNAME, authorities = {"table-semantic-analyse"})
- public void analyseTableColumn_hasRole_succeeds() throws MalformedException, TableNotFoundException,
- DatabaseNotFoundException {
-
- /* test */
- analyseTableColumn_generic(DATABASE_1_ID, TABLE_1_ID, TABLE_1_COLUMNS.get(0).getId(), TABLE_1_COLUMNS.get(0));
- }
-
@Test
@WithAnonymousUser
public void update_publicAnonymous_fails() {
@@ -837,34 +774,6 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
/* ## GENERIC TEST CASES ## */
/* ################################################################################################### */
- public void analyseTable_generic(Long databaseId, Long tableId, Table table) throws MalformedException,
- TableNotFoundException, DatabaseNotFoundException {
-
- /* mock */
- when(entityService.suggestByTable(table))
- .thenReturn(List.of());
-
- /* test */
- final ResponseEntity<List<EntityDto>> response = tableEndpoint.analyseTable(databaseId, tableId);
- assertEquals(HttpStatus.OK, response.getStatusCode());
- final List<EntityDto> body = response.getBody();
- assertNotNull(body);
- }
-
- public void analyseTableColumn_generic(Long databaseId, Long tableId, Long columnId, TableColumn tableColumn)
- throws MalformedException, TableNotFoundException, DatabaseNotFoundException {
-
- /* mock */
- when(entityService.suggestByColumn(tableColumn))
- .thenReturn(List.of());
-
- /* test */
- final ResponseEntity<List<TableColumnEntityDto>> response = tableEndpoint.analyseTableColumn(databaseId, tableId, columnId);
- assertEquals(HttpStatus.OK, response.getStatusCode());
- final List<TableColumnEntityDto> body = response.getBody();
- assertNotNull(body);
- }
-
protected ResponseEntity<List<TableBriefDto>> generic_list(Long databaseId, Database database, Principal principal,
User user, DatabaseAccess access)
throws NotAllowedException, DatabaseNotFoundException, AccessNotFoundException, UserNotFoundException {
diff --git a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/mvc/PrometheusEndpointMvcTest.java b/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/mvc/PrometheusEndpointMvcTest.java
index d3f75d7060..ce621be569 100644
--- a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/mvc/PrometheusEndpointMvcTest.java
+++ b/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/mvc/PrometheusEndpointMvcTest.java
@@ -446,11 +446,6 @@ public class PrometheusEndpointMvcTest extends AbstractUnitTest {
} catch (Exception e) {
/* ignore */
}
- try {
- ontologyEndpoint.find(ONTOLOGY_1_ID, "thing", null);
- } catch (Exception e) {
- /* ignore */
- }
/* test */
for (String metric : List.of("dbrepo_ontologies_findall", "dbrepo_ontologies_find", "dbrepo_ontologies_create", "dbrepo_ontologies_update", "dbrepo_ontologies_delete", "dbrepo_ontologies_entities_find")) {
@@ -529,21 +524,11 @@ public class PrometheusEndpointMvcTest extends AbstractUnitTest {
} catch (Exception e) {
/* ignore */
}
- try {
- tableEndpoint.analyseTable(DATABASE_1_ID, TABLE_1_ID);
- } catch (Exception e) {
- /* ignore */
- }
try {
tableEndpoint.updateStatistic(DATABASE_1_ID, TABLE_1_ID);
} catch (Exception e) {
/* ignore */
}
- try {
- tableEndpoint.analyseTableColumn(DATABASE_1_ID, TABLE_1_ID, TABLE_1_COLUMNS.get(0).getId());
- } catch (Exception e) {
- /* ignore */
- }
try {
tableEndpoint.update(DATABASE_1_ID, TABLE_1_ID, TABLE_1_COLUMNS.get(3).getId(), request, USER_1_PRINCIPAL);
} catch (Exception e) {
diff --git a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/service/EntityServiceUnitTest.java b/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/service/EntityServiceUnitTest.java
deleted file mode 100644
index fd6ac82762..0000000000
--- a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/service/EntityServiceUnitTest.java
+++ /dev/null
@@ -1,163 +0,0 @@
-package at.tuwien.service;
-
-import at.tuwien.test.AbstractUnitTest;
-import at.tuwien.api.semantics.EntityDto;
-import at.tuwien.api.semantics.TableColumnEntityDto;
-import at.tuwien.exception.*;
-import lombok.extern.log4j.Log4j2;
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Disabled;
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.boot.test.mock.mockito.MockBean;
-import org.springframework.test.context.junit.jupiter.SpringExtension;
-
-import java.util.List;
-
-import static org.junit.jupiter.api.Assertions.*;
-import static org.mockito.ArgumentMatchers.anyString;
-import static org.mockito.Mockito.doThrow;
-import static org.mockito.Mockito.when;
-
-@Log4j2
-@SpringBootTest
-@ExtendWith(SpringExtension.class)
-public class EntityServiceUnitTest extends AbstractUnitTest {
-
- @MockBean
- private OntologyService ontologyService;
-
- @Autowired
- private EntityService entityService;
-
- @BeforeEach
- public void beforeEach() {
- genesis();
- }
-
- @Test
- public void findByLabel_wikidataSparql_succeeds() throws MalformedException {
-
- /* mock */
- when(ontologyService.findAll())
- .thenReturn(List.of(ONTOLOGY_1, ONTOLOGY_2, ONTOLOGY_3, ONTOLOGY_4));
-
- /* test */
- final List<EntityDto> response = entityService.findByLabel(ONTOLOGY_2, "temperature");
- assertFalse(response.isEmpty());
- final EntityDto entity0 = response.get(0);
- assertNotNull(entity0.getUri());
- log.trace("found concept {}", entity0);
- }
-
- @Test
- public void findByUri_wikidataSparql_succeeds() throws MalformedException, OntologyNotFoundException {
-
- /* mock */
- when(ontologyService.find(CONCEPT_1_URI))
- .thenReturn(ONTOLOGY_1);
- when(ontologyService.findAll())
- .thenReturn(List.of(ONTOLOGY_1, ONTOLOGY_2, ONTOLOGY_3, ONTOLOGY_4));
-
- /* test */
- final List<EntityDto> response = entityService.findByUri(CONCEPT_1_URI);
- assertEquals(1, response.size());
- final EntityDto entity0 = response.get(0);
- assertNotNull(entity0.getUri());
- log.trace("found concept {}", entity0);
- }
-
- @Test
- public void findOneByUri_wikidataSparql_succeeds() throws MalformedException, SemanticEntityNotFoundException,
- OntologyNotFoundException {
-
- /* mock */
- when(ontologyService.find(CONCEPT_1_URI))
- .thenReturn(ONTOLOGY_1);
- when(ontologyService.findAll())
- .thenReturn(List.of(ONTOLOGY_1, ONTOLOGY_2, ONTOLOGY_3, ONTOLOGY_4));
-
- /* test */
- final EntityDto response = entityService.findOneByUri(CONCEPT_1_URI);
- assertNotNull(response.getUri());
- log.trace("found concept {}", response);
- }
-
- @Test
- public void findByLabel_om2Rdf_succeeds() throws MalformedException {
-
- /* mock */
- when(ontologyService.findAll())
- .thenReturn(List.of(ONTOLOGY_1, ONTOLOGY_2, ONTOLOGY_3, ONTOLOGY_4));
-
- /* test */
- final List<EntityDto> response = entityService.findByLabel(ONTOLOGY_1, "millimetre");
- assertFalse(response.isEmpty());
- final EntityDto entity0 = response.get(0);
- assertNotNull(entity0.getUri());
- log.trace("found unit {}", entity0);
- }
-
- @Test
- public void findByUri_om2Rdf_succeeds() throws MalformedException, OntologyNotFoundException {
-
- /* mock */
- when(ontologyService.find(UNIT_1_URI))
- .thenReturn(ONTOLOGY_1);
- when(ontologyService.findAll())
- .thenReturn(List.of(ONTOLOGY_1, ONTOLOGY_2, ONTOLOGY_3, ONTOLOGY_4, ONTOLOGY_5));
-
- /* test */
- final List<EntityDto> response = entityService.findByUri(UNIT_1_URI);
- assertEquals(1, response.size());
- final EntityDto entity0 = response.get(0);
- assertNotNull(entity0.getUri());
- log.trace("found unit {}", entity0);
- }
-
- @Test
- @Disabled("integration")
- public void suggestByTable_succeeds() throws MalformedException {
-
- /* mock */
- when(ontologyService.findAll())
- .thenReturn(List.of(ONTOLOGY_1, ONTOLOGY_2, ONTOLOGY_3, ONTOLOGY_4, ONTOLOGY_5));
- when(ontologyService.findAllProcessable())
- .thenReturn(List.of(ONTOLOGY_2, ONTOLOGY_5));
-
- /* test */
- final List<EntityDto> response = entityService.suggestByTable(TABLE_2);
- assertEquals(1, response.size());
- }
-
- @Test
- public void suggestTableColumnSemantics_succeeds() throws MalformedException {
-
- /* mock */
- when(ontologyService.findAll())
- .thenReturn(List.of(ONTOLOGY_1, ONTOLOGY_2, ONTOLOGY_3, ONTOLOGY_4, ONTOLOGY_5));
- when(ontologyService.findAllProcessable())
- .thenReturn(List.of(ONTOLOGY_2, ONTOLOGY_5));
-
- /* test */
- final List<TableColumnEntityDto> response = entityService.suggestByColumn(TABLE_1_COLUMNS.get(0));
- assertFalse(response.isEmpty());
- }
-
- @Test
- public void findByUri_noRdfNoSparql_fails() throws OntologyNotFoundException {
-
- /* mock */
- doThrow(OntologyNotFoundException.class)
- .when(ontologyService)
- .find(anyString());
-
- /* test */
- assertThrows(OntologyNotFoundException.class, () -> {
- entityService.findByUri("http://schema.org/MedicalCondition");
- });
- }
-
-}
diff --git a/dbrepo-metadata-service/services/src/main/java/at/tuwien/service/EntityService.java b/dbrepo-metadata-service/services/src/main/java/at/tuwien/service/EntityService.java
deleted file mode 100644
index 69a801cf5c..0000000000
--- a/dbrepo-metadata-service/services/src/main/java/at/tuwien/service/EntityService.java
+++ /dev/null
@@ -1,64 +0,0 @@
-package at.tuwien.service;
-
-import at.tuwien.api.semantics.EntityDto;
-import at.tuwien.api.semantics.TableColumnEntityDto;
-import at.tuwien.entities.database.table.Table;
-import at.tuwien.entities.database.table.columns.TableColumn;
-import at.tuwien.entities.semantics.Ontology;
-import at.tuwien.exception.*;
-
-import java.util.List;
-
-public interface EntityService {
-
- /**
- * Finds entities in the ontology whose label match the given label.
- *
- * @param ontology The ontology.
- * @param label The label.
- * @return The list of entities that match.
- */
- List<EntityDto> findByLabel(Ontology ontology, String label) throws MalformedException;
-
- /**
- * Finds entities in the ontology whose label match the given label with maximum number of entities.
- *
- * @param ontology The ontology.
- * @param label The label.
- * @param limit The maximum number of entities to return.
- * @return The list of entities that match.
- */
- List<EntityDto> findByLabel(Ontology ontology, String label, Integer limit) throws MalformedException;
-
- /**
- * Finds entities in the ontology whose uri match the given uri.
- *
- * @param uri The uri.
- * @return The list of entities that match.
- */
- List<EntityDto> findByUri(String uri) throws MalformedException, OntologyNotFoundException;
-
- /**
- * Finds an entity in the ontology whose uri match the given uri.
- *
- * @param uri The uri.
- * @return The entity, if successful.
- */
- EntityDto findOneByUri(String uri) throws MalformedException, SemanticEntityNotFoundException, OntologyNotFoundException;
-
- /**
- * Attempts to suggest table semantics for a table with given id in database with given id.
- *
- * @param table The table.
- * @return The list of entities that were suggested.
- */
- List<EntityDto> suggestByTable(Table table) throws MalformedException;
-
- /**
- * Attempts to suggest table column semantics for a table column in table with given id in database with given id.
- *
- * @param column The table column.
- * @return The list of entities that were suggested.
- */
- List<TableColumnEntityDto> suggestByColumn(TableColumn column) throws MalformedException;
-}
diff --git a/dbrepo-metadata-service/services/src/main/java/at/tuwien/service/impl/EntityServiceImpl.java b/dbrepo-metadata-service/services/src/main/java/at/tuwien/service/impl/EntityServiceImpl.java
deleted file mode 100644
index dba30481f5..0000000000
--- a/dbrepo-metadata-service/services/src/main/java/at/tuwien/service/impl/EntityServiceImpl.java
+++ /dev/null
@@ -1,167 +0,0 @@
-package at.tuwien.service.impl;
-
-import at.tuwien.api.semantics.EntityDto;
-import at.tuwien.api.semantics.TableColumnEntityDto;
-import at.tuwien.config.JenaConfig;
-import at.tuwien.entities.database.table.Table;
-import at.tuwien.entities.database.table.columns.TableColumn;
-import at.tuwien.entities.semantics.Ontology;
-import at.tuwien.exception.*;
-import at.tuwien.mapper.SparqlMapper;
-import at.tuwien.service.EntityService;
-import at.tuwien.service.OntologyService;
-import lombok.extern.log4j.Log4j2;
-import org.apache.jena.query.*;
-import org.apache.jena.rdf.model.RDFNode;
-import org.apache.jena.riot.RDFDataMgr;
-import org.apache.jena.riot.RiotException;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Service;
-import org.springframework.transaction.annotation.Transactional;
-
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.concurrent.TimeUnit;
-
-@Log4j2
-@Service
-public class EntityServiceImpl implements EntityService {
-
- private final Dataset dataset;
- private final JenaConfig jenaConfig;
- private final SparqlMapper ontologyMapper;
- private final OntologyService ontologyService;
-
- @Autowired
- public EntityServiceImpl(Dataset dataset, JenaConfig jenaConfig, SparqlMapper ontologyMapper,
- OntologyService ontologyService) {
- this.dataset = dataset;
- this.jenaConfig = jenaConfig;
- this.ontologyMapper = ontologyMapper;
- this.ontologyService = ontologyService;
- }
-
- public void validateOntology(Ontology ontology) throws MalformedException {
- if (ontology.getRdfPath() == null && ontology.getSparqlEndpoint() == null) {
- log.error("Ontology with uri {} is invalid: no RDF file present and no SPARQL endpoint found", ontology.getUri());
- throw new MalformedException("Ontology with uri " + ontology.getUri() + " is invalid: no RDF file present and no SPARQL endpoint found");
- }
- }
-
- @Override
- public List<EntityDto> findByLabel(Ontology ontology, String label) throws MalformedException {
- return findByLabel(ontology, label, 10);
- }
-
- @Override
- public List<EntityDto> findByLabel(Ontology ontology, String label, Integer limit) throws MalformedException {
- /* check */
- validateOntology(ontology);
- /* find */
- final List<Ontology> ontologies = ontologyService.findAll();
- final String statement = ontologyMapper.ontologyToFindByLabelQuery(ontologies, ontology, label, limit);
- log.trace("execute sparql query:\n{}", statement);
- final List<EntityDto> results = new LinkedList<>();
- if (ontology.getSparqlEndpoint() == null && ontology.getRdfPath() != null) {
- log.debug("load rdf model from path {}", ontology.getRdfPath());
- this.dataset.setDefaultModel(RDFDataMgr.loadModel(ontology.getRdfPath()));
- }
- try (QueryExecution execution = QueryExecutionDatasetBuilder.create()
- .model(this.dataset.getDefaultModel())
- .query(statement)
- .timeout(jenaConfig.getConnectionTimeout(), TimeUnit.MILLISECONDS)
- .build()) {
- final Iterator<QuerySolution> resultSet = execution.execSelect();
- while (resultSet.hasNext()) {
- final QuerySolution solution = resultSet.next();
- final RDFNode description = solution.get("description");
- final EntityDto entity = EntityDto.builder()
- .uri(solution.get("o").toString())
- .label(label)
- .description(description != null ? description.asLiteral().getLexicalForm() : null)
- .build();
- results.add(entity);
- }
- } catch (QueryParseException | IllegalArgumentException | RiotException e) {
- log.error("Failed to parse query: {}", e.getMessage());
- throw new MalformedException("Failed to parse query: " + e.getMessage(), e);
- }
- return results;
- }
-
- @Override
- public List<EntityDto> findByUri(String uri) throws MalformedException, OntologyNotFoundException {
- /* find */
- final Ontology ontology = ontologyService.find(uri);
- final List<Ontology> ontologies = ontologyService.findAll();
- final String statement = ontologyMapper.ontologyToFindByUriQuery(ontologies, ontology, uri);
- log.trace("execute sparql query:\n{}", statement);
- try (QueryExecution execution = QueryExecutionDatasetBuilder.create()
- .model(this.dataset.getDefaultModel())
- .query(statement)
- .timeout(jenaConfig.getConnectionTimeout(), TimeUnit.MILLISECONDS)
- .build()) {
- final Iterator<QuerySolution> resultSet = execution.execSelect();
- final List<EntityDto> results = new LinkedList<>();
- while (resultSet.hasNext()) {
- final QuerySolution solution = resultSet.next();
- final RDFNode label = solution.get("label");
- final RDFNode description = solution.get("description");
- final EntityDto entity = EntityDto.builder()
- .uri(uri)
- .label(label != null ? label.asLiteral().getLexicalForm() : null)
- .description(description != null ? description.asLiteral().getLexicalForm() : null)
- .build();
- results.add(entity);
- }
- return results;
- } catch (QueryParseException | IllegalArgumentException | RiotException e) {
- log.error("Failed to parse query: {}", e.getMessage());
- throw new MalformedException("Failed to parse query: " + e.getMessage(), e);
- }
- }
-
- @Override
- public EntityDto findOneByUri(String uri) throws MalformedException, SemanticEntityNotFoundException,
- OntologyNotFoundException {
- /* find */
- final List<EntityDto> results = findByUri(uri);
- if (results.size() != 1) {
- log.error("None or multiple entities found for uri {}", uri);
- throw new SemanticEntityNotFoundException("None or multiple entities found for uri " + uri);
- }
- return results.get(0);
- }
-
- @Override
- @Transactional(readOnly = true)
- public List<EntityDto> suggestByTable(Table table) throws MalformedException {
- final List<EntityDto> suggestions = new LinkedList<>();
- for (Ontology ontology : ontologyService.findAllProcessable()) {
- suggestions.addAll(findByLabel(ontology, table.getName(), 3));
- }
- return suggestions;
- }
-
- @Override
- @Transactional(readOnly = true)
- public List<TableColumnEntityDto> suggestByColumn(TableColumn tableColumn) throws MalformedException {
- final List<TableColumnEntityDto> suggestions = new LinkedList<>();
- for (Ontology ontology : ontologyService.findAllProcessable()) {
- suggestions.addAll(findByLabel(ontology, tableColumn.getName(), 3)
- .stream()
- .map(e -> TableColumnEntityDto.builder()
- .databaseId(tableColumn.getTable().getDatabase().getId())
- .tableId(tableColumn.getTable().getId())
- .columnId(tableColumn.getId())
- .label(e.getLabel())
- .uri(e.getUri())
- .description(e.getDescription())
- .build())
- .toList());
- }
- return suggestions;
- }
-
-}
diff --git a/dbrepo-metadata-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java b/dbrepo-metadata-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java
index 7ca855974e..8572372516 100644
--- a/dbrepo-metadata-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java
+++ b/dbrepo-metadata-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java
@@ -6,6 +6,7 @@ import at.tuwien.api.database.table.columns.ColumnCreateDto;
import at.tuwien.api.database.table.columns.ColumnStatisticDto;
import at.tuwien.api.database.table.columns.ColumnTypeDto;
import at.tuwien.api.database.table.columns.concepts.ColumnSemanticsUpdateDto;
+import at.tuwien.api.semantics.EntityDto;
import at.tuwien.config.RabbitConfig;
import at.tuwien.entities.container.image.ContainerImageDate;
import at.tuwien.entities.database.Database;
@@ -36,7 +37,6 @@ public class TableServiceImpl implements TableService {
private final UserService userService;
private final UnitService unitService;
private final RabbitConfig rabbitConfig;
- private final EntityService entityService;
private final ConceptService conceptService;
private final MetadataMapper metadataMapper;
private final DatabaseService databaseService;
@@ -46,13 +46,12 @@ public class TableServiceImpl implements TableService {
@Autowired
public TableServiceImpl(UserService userService, UnitService unitService, RabbitConfig rabbitConfig,
- EntityService entityService, ConceptService conceptService, MetadataMapper metadataMapper,
+ ConceptService conceptService, MetadataMapper metadataMapper,
DatabaseService databaseService, DataServiceGateway dataServiceGateway,
DatabaseRepository databaseRepository, SearchServiceGateway searchServiceGateway) {
this.userService = userService;
this.unitService = unitService;
this.rabbitConfig = rabbitConfig;
- this.entityService = entityService;
this.conceptService = conceptService;
this.metadataMapper = metadataMapper;
this.databaseService = databaseService;
@@ -128,23 +127,31 @@ public class TableServiceImpl implements TableService {
column.setTable(table);
if (c.getUnitUri() != null) {
log.trace("column {} has assigned unit uri: {}", column.getInternalName(), c.getUnitUri());
- TableColumnUnit unit;
try {
- unit = unitService.find(c.getUnitUri());
+ column.setUnit(unitService.find(c.getUnitUri()));
+ log.debug("found unit by uri: {}", c.getUnitUri());
} catch (UnitNotFoundException e) {
- unit = unitService.create(metadataMapper.entityDtoToTableColumnUnit(entityService.findOneByUri(c.getUnitUri())));
+ final TableColumnUnit unit = metadataMapper.entityDtoToTableColumnUnit(EntityDto.builder()
+ .uri(c.getUnitUri())
+ .label(c.getUnitLabel())
+ .build());
+ column.setUnit(unitService.create(unit));
+ log.trace("created unit in metadata database: {}", unit);
}
- column.setUnit(unit);
}
if (c.getConceptUri() != null) {
log.trace("column {} has assigned concept uri: {}", column.getInternalName(), c.getConceptUri());
- TableColumnConcept concept;
try {
- concept = conceptService.find(c.getConceptUri());
+ column.setConcept(conceptService.find(c.getConceptUri()));
+ log.debug("found concept by uri: {}", c.getConceptUri());
} catch (ConceptNotFoundException e) {
- concept = conceptService.create(metadataMapper.entityDtoToTableColumnConcept(entityService.findOneByUri(c.getConceptUri())));
+ final TableColumnConcept concept = metadataMapper.entityDtoToTableColumnConcept(EntityDto.builder()
+ .uri(c.getConceptUri())
+ .label(c.getConceptLabel())
+ .build());
+ column.setConcept(conceptService.create(concept));
+ log.trace("created concept in metadata database: {}", concept);
}
- column.setConcept(concept);
}
if (List.of(TableColumnType.TIME, TableColumnType.TIMESTAMP, TableColumnType.DATE, TableColumnType.DATETIME).contains(column.getColumnType())) {
final Optional<ContainerImageDate> optional = database.getContainer()
@@ -218,24 +225,32 @@ public class TableServiceImpl implements TableService {
SemanticEntityNotFoundException {
/* assign */
if (data.getUnitUri() != null) {
- TableColumnUnit unit;
try {
- unit = unitService.find(data.getUnitUri());
+ column.setUnit(unitService.find(data.getUnitUri()));
+ log.debug("found unit by uri: {}", data.getUnitUri());
} catch (UnitNotFoundException e) {
- unit = metadataMapper.entityDtoToTableColumnUnit(entityService.findOneByUri(data.getUnitUri()));
+ final TableColumnUnit unit = metadataMapper.entityDtoToTableColumnUnit(EntityDto.builder()
+ .uri(data.getUnitUri())
+ .label(data.getUnitLabel())
+ .build());
+ log.trace("create unit in metadata database: {}", unit);
+ column.setUnit(unit);
}
- column.setUnit(unit);
} else {
column.setUnit(null);
}
if (data.getConceptUri() != null) {
- TableColumnConcept concept;
try {
- concept = conceptService.find(data.getConceptUri());
+ conceptService.find(data.getConceptUri());
+ log.debug("found concept by uri: {}", data.getConceptUri());
} catch (ConceptNotFoundException e) {
- concept = metadataMapper.entityDtoToTableColumnConcept(entityService.findOneByUri(data.getConceptUri()));
+ final TableColumnConcept concept = metadataMapper.entityDtoToTableColumnConcept(EntityDto.builder()
+ .uri(data.getConceptUri())
+ .label(data.getConceptLabel())
+ .build());
+ log.trace("create concept in metadata database: {}", concept);
+ column.setConcept(concept);
}
- column.setConcept(concept);
} else {
column.setConcept(null);
}
diff --git a/dbrepo-ui/components/table/TableSchema.vue b/dbrepo-ui/components/table/TableSchema.vue
index 845039b136..8539962de5 100644
--- a/dbrepo-ui/components/table/TableSchema.vue
+++ b/dbrepo-ui/components/table/TableSchema.vue
@@ -149,11 +149,12 @@
cols="1">
<v-select
v-if="c.concepts"
- v-model="c.concept_uri"
+ v-model="c.concept"
persistent-hint
+ :items="c.concepts"
:item-title="item => `${item.name} (${item.ontology})`"
item-value="uri"
- :items="c.concepts"
+ return-object
:label="$t('pages.table.subpages.schema.concept.label')"
:hint="$t('pages.table.subpages.schema.concept.hint')"
:id="'object' + c.name"
@@ -169,11 +170,12 @@
cols="1">
<v-select
v-if="c.units"
- v-model="c.unit_uri"
+ v-model="c.unit"
persistent-hint
+ :items="c.units"
:item-title="item => `${item.name} (${item.ontology})`"
item-value="uri"
- :items="c.units"
+ return-object
:label="$t('pages.table.subpages.schema.unit.label')"
:hint="$t('pages.table.subpages.schema.unit.hint')"
:id="'unit' + c.name"
@@ -423,9 +425,9 @@ export default {
name,
type,
concepts: [],
- concept_uri: null,
+ concept: null,
units: [],
- unit_uri: null,
+ unit: null,
null_allowed,
primary_key,
dfid: null,
diff --git a/dbrepo-ui/composables/table-service.ts b/dbrepo-ui/composables/table-service.ts
index d26fbce900..52959d33c0 100644
--- a/dbrepo-ui/composables/table-service.ts
+++ b/dbrepo-ui/composables/table-service.ts
@@ -187,22 +187,6 @@ export const useTableService = (): any => {
});
}
- async function suggest(databaseId: number, tableId: number, columnId: number): Promise<TableColumnEntityDto[]> {
- const axios = useAxiosInstance()
- console.debug('suggest semantic entities for table column with id', columnId, 'of table with id', tableId, 'of database with id', databaseId)
- return new Promise<TableColumnEntityDto[]>((resolve, reject) => {
- axios.get<TableColumnEntityDto[]>(`/api/database/${databaseId}/table/${tableId}/column/${columnId}/suggest`)
- .then((response) => {
- console.info('Suggested semantic entities for table column with id', columnId, 'of table with id', tableId, 'of database with id', databaseId)
- resolve(response.data)
- })
- .catch((error) => {
- console.error('Failed to suggest semantic entities', error)
- reject(axiosErrorToApiError(error))
- })
- })
- }
-
function prepareColumns(columns: InternalColumnDto[]): ColumnCreateDto[] {
return columns.map((c: InternalColumnDto) => {
const column: ColumnCreateDto = {
@@ -215,8 +199,10 @@ export const useTableService = (): any => {
sets: c.sets_values ? c.sets_values.split(',') : [],
index_length: c.index_length,
null_allowed: c.null_allowed,
- concept_uri: c.concept_uri ? c.concept_uri : null,
- unit_uri: c.unit_uri ? c.unit_uri : null
+ concept_uri: c.concept?.uri ? c.concept.uri : null,
+ concept_label: c.concept?.name ? c.concept.name : null,
+ unit_uri: c.unit?.uri ? c.unit.uri : null,
+ unit_label: c.unit?.name ? c.unit.name : null
}
return column
})
@@ -271,7 +257,6 @@ export const useTableService = (): any => {
remove,
removeTuple,
history,
- suggest,
prepareColumns,
prepareConstraints,
isOwner,
diff --git a/dbrepo-ui/dto/index.ts b/dbrepo-ui/dto/index.ts
index 4aff532930..e6cb7ffbe3 100644
--- a/dbrepo-ui/dto/index.ts
+++ b/dbrepo-ui/dto/index.ts
@@ -639,11 +639,20 @@ interface ColumnCreateDto {
enums: string[];
sets: string[];
unit_uri: string | null;
+ unit_label: string | null;
concept_uri: string | null;
+ concept_label: string | null;
index_length: number;
null_allowed: boolean;
}
+interface EntityDto {
+ name: string | null;
+ score: number;
+ uri: string;
+ ontology: string;
+}
+
interface InternalColumnDto {
name: string;
type: string;
@@ -652,6 +661,8 @@ interface InternalColumnDto {
dfid: number;
enums: string[];
sets: string[];
+ unit: EntityDto | null;
+ concept: EntityDto | null;
primary_key: boolean;
index_length: number;
null_allowed: boolean;
--
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