diff --git a/dbrepo-metadata-db/setup-schema.sql b/dbrepo-metadata-db/setup-schema.sql
index 92afa5c8ca4f93d3b57e414d550db32abd24c335..737ef8e464c454a171e53150f19bd98ed9cff20a 100644
--- a/dbrepo-metadata-db/setup-schema.sql
+++ b/dbrepo-metadata-db/setup-schema.sql
@@ -502,7 +502,7 @@ VALUES (1, '%Y-%c-%d %H:%i:%S.%f', 'yyyy-MM-dd HH:mm:ss.SSSSSS', '2022-01-30 13:
(1, '%Y-%c-%d', 'yyyy-MM-dd', '2022-01-30', false);
INSERT INTO `fda`.`mdb_ontologies` (prefix, uri, sparql_endpoint)
-VALUES ('om2', 'http://www.ontology-of-units-of-measure.org/resource/om-2/', null),
+VALUES ('om', 'http://www.ontology-of-units-of-measure.org/resource/om-2/', null),
('wd', 'http://www.wikidata.org/', 'https://query.wikidata.org/sparql'),
('mo', 'http://purl.org/ontology/mo/', null),
('dc', 'http://purl.org/dc/elements/1.1/', null),
diff --git a/dbrepo-metadata-db/test/src/main/java/at/tuwien/test/BaseTest.java b/dbrepo-metadata-db/test/src/main/java/at/tuwien/test/BaseTest.java
index 29951cebd09fc50900586e310634e30d1e0e2a17..13c1cee40c5eded82ceec8d0e3ea84ca25e421e7 100644
--- a/dbrepo-metadata-db/test/src/main/java/at/tuwien/test/BaseTest.java
+++ b/dbrepo-metadata-db/test/src/main/java/at/tuwien/test/BaseTest.java
@@ -1879,6 +1879,26 @@ public abstract class BaseTest {
.sparqlEndpoint(ONTOLOGY_4_SPARQL_ENDPOINT)
.build();
+ public final static Long ONTOLOGY_5_ID = 5L;
+ public final static String ONTOLOGY_5_PREFIX = "db";
+ public final static String ONTOLOGY_5_URI = "http://dbpedia.org";
+ public final static String ONTOLOGY_5_SPARQL_ENDPOINT = "http://dbpedia.org/sparql";
+ public final static UUID ONTOLOGY_5_CREATED_BY = USER_1_ID;
+
+ public final static Ontology ONTOLOGY_5 = Ontology.builder()
+ .id(ONTOLOGY_5_ID)
+ .prefix(ONTOLOGY_5_PREFIX)
+ .uri(ONTOLOGY_5_URI)
+ .sparqlEndpoint(ONTOLOGY_5_SPARQL_ENDPOINT)
+ .createdBy(ONTOLOGY_5_CREATED_BY)
+ .build();
+
+ public final static OntologyCreateDto ONTOLOGY_5_CREATE_DTO = OntologyCreateDto.builder()
+ .prefix(ONTOLOGY_5_PREFIX)
+ .uri(ONTOLOGY_5_URI)
+ .sparqlEndpoint(ONTOLOGY_5_SPARQL_ENDPOINT)
+ .build();
+
public final static String COLUMN_CONCEPT_TEMPERATURE_NAME = "temperature";
public final static String COLUMN_CONCEPT_TEMPERATURE_URI = "http://www.wikidata.org/entity/Q11466";
public final static String COLUMN_CONCEPT_TEMPERATURE_DESCRIPTION = "physical property of matter that quantitatively expresses the common notions of hot and cold";
diff --git a/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/OntologyEndpoint.java b/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/OntologyEndpoint.java
index 74433460a69c41526af16f95d01cf3811ce80945..36d60d66b3073021c82f8bf66433db62325d7724 100644
--- a/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/OntologyEndpoint.java
+++ b/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/OntologyEndpoint.java
@@ -3,6 +3,7 @@ package at.tuwien.endpoints;
import at.tuwien.api.error.ApiErrorDto;
import at.tuwien.api.semantics.*;
import at.tuwien.exception.OntologyNotFoundException;
+import at.tuwien.exception.UserNotFoundException;
import at.tuwien.mapper.OntologyMapper;
import at.tuwien.service.OntologyService;
import io.micrometer.core.annotation.Timed;
@@ -93,11 +94,16 @@ public class OntologyEndpoint {
content = {@Content(
mediaType = "application/json",
schema = @Schema(implementation = OntologyDto.class))}),
+ @ApiResponse(responseCode = "201",
+ description = "Could not find user",
+ content = {@Content(
+ mediaType = "application/json",
+ schema = @Schema(implementation = ApiErrorDto.class))}),
})
public ResponseEntity<OntologyDto> create(@NotNull @Valid @RequestBody OntologyCreateDto data,
- @NotNull Principal principal) {
+ @NotNull Principal principal) throws UserNotFoundException {
log.debug("endpoint create ontology, data={}, principal={}", data, principal);
- final OntologyDto dto = ontologyMapper.ontologyToOntologyDto(ontologyService.create(data));
+ final OntologyDto dto = ontologyMapper.ontologyToOntologyDto(ontologyService.create(data, principal));
log.trace("create ontology resulted in dto {}", dto);
return ResponseEntity.status(HttpStatus.CREATED)
.body(dto);
diff --git a/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/QueryEndpoint.java b/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/QueryEndpoint.java
index 9d1ed742fbf29dc6434f17767c4b77fa8378bf3a..159f8c1eceaf230412dbacc1099f2c16675608b4 100644
--- a/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/QueryEndpoint.java
+++ b/dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/QueryEndpoint.java
@@ -82,6 +82,10 @@ public class QueryEndpoint {
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) {
diff --git a/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/endpoint/OntologyEndpointUnitTest.java b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/endpoint/OntologyEndpointUnitTest.java
index a412b6c965b80dd7f89af1cc64db20d9d1accab2..00ad512534c9cc5dea5bd3a6bc7f369914c60012 100644
--- a/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/endpoint/OntologyEndpointUnitTest.java
+++ b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/endpoint/OntologyEndpointUnitTest.java
@@ -8,8 +8,11 @@ import at.tuwien.api.semantics.OntologyDto;
import at.tuwien.api.semantics.OntologyModifyDto;
import at.tuwien.endpoints.OntologyEndpoint;
import at.tuwien.entities.semantics.Ontology;
+import at.tuwien.entities.user.User;
import at.tuwien.exception.OntologyNotFoundException;
+import at.tuwien.exception.UserNotFoundException;
import at.tuwien.service.OntologyService;
+import at.tuwien.service.UserService;
import lombok.extern.log4j.Log4j2;
import org.apache.jena.sys.JenaSystem;
import org.hibernate.HibernateException;
@@ -43,6 +46,9 @@ public class OntologyEndpointUnitTest extends BaseUnitTest {
@MockBean
private OntologyService ontologyService;
+ @MockBean
+ private UserService userService;
+
@BeforeAll
public static void beforeAll() {
JenaSystem.init();
@@ -96,7 +102,7 @@ public class OntologyEndpointUnitTest extends BaseUnitTest {
/* test */
assertThrows(AccessDeniedException.class, () -> {
- create_generic(ONTOLOGY_1_CREATE_DTO, null, ONTOLOGY_1);
+ create_generic(ONTOLOGY_1_CREATE_DTO, null, null, null, ONTOLOGY_1);
});
}
@@ -106,16 +112,16 @@ public class OntologyEndpointUnitTest extends BaseUnitTest {
/* test */
assertThrows(AccessDeniedException.class, () -> {
- create_generic(ONTOLOGY_1_CREATE_DTO, USER_4_PRINCIPAL, ONTOLOGY_1);
+ create_generic(ONTOLOGY_1_CREATE_DTO, USER_4_PRINCIPAL, USER_4_USERNAME, USER_4, ONTOLOGY_1);
});
}
@Test
@WithMockUser(username = USER_3_USERNAME, authorities = {"create-ontology"})
- public void create_hasRole_succeeds() {
+ public void create_hasRole_succeeds() throws UserNotFoundException {
/* test */
- create_generic(ONTOLOGY_1_CREATE_DTO, USER_3_PRINCIPAL, ONTOLOGY_1);
+ create_generic(ONTOLOGY_1_CREATE_DTO, USER_3_PRINCIPAL, USER_3_USERNAME, USER_3, ONTOLOGY_1);
}
@Test
@@ -231,16 +237,25 @@ public class OntologyEndpointUnitTest extends BaseUnitTest {
assertNotNull(body);
}
- public void create_generic(OntologyCreateDto createDto, Principal principal, Ontology ontology) {
+ public void create_generic(OntologyCreateDto createDto, Principal principal, String username, User user, Ontology ontology)
+ throws UserNotFoundException {
/* mock */
if (ontology != null) {
- when(ontologyService.create(createDto))
+ when(ontologyService.create(createDto, principal))
.thenReturn(ontology);
} else {
doThrow(HibernateException.class)
.when(ontologyService)
- .create(createDto);
+ .create(createDto, principal);
+ }
+ if (user != null) {
+ when(userService.findByUsername(username))
+ .thenReturn(user);
+ } else {
+ doThrow(UserNotFoundException.class)
+ .when(userService)
+ .findByUsername(username);
}
/* test */
diff --git a/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/endpoint/SemanticsEndpointUnitTest.java b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/endpoint/SemanticsEndpointUnitTest.java
index d140d7fb1a79905e9ff0142f1924196725c30fe9..64adc9cad1b3c64acac9f5c92a3912355f395466 100644
--- a/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/endpoint/SemanticsEndpointUnitTest.java
+++ b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/endpoint/SemanticsEndpointUnitTest.java
@@ -129,13 +129,11 @@ public class SemanticsEndpointUnitTest extends BaseUnitTest {
}
@Test
- @WithMockUser(username = USER_3_USERNAME, authorities = {"create-semantic-concept"})
+ @WithMockUser(username = USER_3_USERNAME, authorities = {"create-semantic-unit"})
public void saveUnit_hasRole_succeeds() {
/* test */
- assertThrows(AccessDeniedException.class, () -> {
- saveUnit_generic(COLUMN_UNIT_DEGREES_CELSIUS_SAVE_DTO, COLUMN_UNIT_DEGREES_CELSIUS);
- });
+ saveUnit_generic(COLUMN_UNIT_DEGREES_CELSIUS_SAVE_DTO, COLUMN_UNIT_DEGREES_CELSIUS);
}
/* ################################################################################################### */
diff --git a/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/endpoint/TableEndpointUnitTest.java b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/endpoint/TableEndpointUnitTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..cd5dc23cd807c7e066fa80796a28a1a0917e8212
--- /dev/null
+++ b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/endpoint/TableEndpointUnitTest.java
@@ -0,0 +1,139 @@
+
+package at.tuwien.endpoint;
+
+import at.tuwien.BaseUnitTest;
+import at.tuwien.api.semantics.*;
+import at.tuwien.endpoints.OntologyEndpoint;
+import at.tuwien.endpoints.TableEndpoint;
+import at.tuwien.entities.semantics.Ontology;
+import at.tuwien.exception.OntologyNotFoundException;
+import at.tuwien.exception.QueryMalformedException;
+import at.tuwien.exception.TableColumnNotFoundException;
+import at.tuwien.exception.TableNotFoundException;
+import at.tuwien.service.OntologyService;
+import at.tuwien.service.TableService;
+import lombok.extern.log4j.Log4j2;
+import org.apache.jena.sys.JenaSystem;
+import org.hibernate.HibernateException;
+import org.junit.jupiter.api.BeforeAll;
+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.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.security.access.AccessDeniedException;
+import org.springframework.security.test.context.support.WithAnonymousUser;
+import org.springframework.security.test.context.support.WithMockUser;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
+
+import java.security.Principal;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.*;
+import static org.mockito.Mockito.*;
+
+@Log4j2
+@SpringBootTest
+@ExtendWith(SpringExtension.class)
+public class TableEndpointUnitTest extends BaseUnitTest {
+
+ @Autowired
+ private TableEndpoint tableEndpoint;
+
+ @MockBean
+ private TableService tableService;
+
+ @BeforeAll
+ public static void beforeAll() {
+ JenaSystem.init();
+ }
+
+ @Test
+ @WithAnonymousUser
+ public void analyseTable_anonymous_fails() {
+
+ /* test */
+ assertThrows(AccessDeniedException.class, () -> {
+ analyseTable_generic(DATABASE_1_ID, TABLE_1_ID);
+ });
+ }
+
+ @Test
+ @WithMockUser(username = USER_4_USERNAME)
+ public void findAll_noRole_fails() {
+
+ /* test */
+ assertThrows(AccessDeniedException.class, () -> {
+ analyseTable_generic(DATABASE_1_ID, TABLE_1_ID);
+ });
+ }
+
+ @Test
+ @WithMockUser(username = USER_1_USERNAME, authorities = {"table-semantic-analyse"})
+ public void findAll_hasRole_succeeds() throws TableNotFoundException, QueryMalformedException {
+
+ /* test */
+ analyseTable_generic(DATABASE_1_ID, TABLE_1_ID);
+ }
+
+ @Test
+ @WithAnonymousUser
+ public void analyseTableColumn_anonymous_fails() {
+
+ /* test */
+ assertThrows(AccessDeniedException.class, () -> {
+ analyseTableColumn_generic(DATABASE_1_ID, TABLE_1_ID, COLUMN_1_1_ID);
+ });
+ }
+
+ @Test
+ @WithMockUser(username = USER_4_USERNAME)
+ public void analyseTableColumn_noRole_fails() {
+
+ /* test */
+ assertThrows(AccessDeniedException.class, () -> {
+ analyseTableColumn_generic(DATABASE_1_ID, TABLE_1_ID, COLUMN_1_1_ID);
+ });
+ }
+
+ @Test
+ @WithMockUser(username = USER_1_USERNAME, authorities = {"table-semantic-analyse"})
+ public void analyseTableColumn_hasRole_succeeds() throws QueryMalformedException, TableColumnNotFoundException {
+
+ /* test */
+ analyseTableColumn_generic(DATABASE_1_ID, TABLE_1_ID, COLUMN_1_1_ID);
+ }
+
+ /* ################################################################################################### */
+ /* ## GENERIC TEST CASES ## */
+ /* ################################################################################################### */
+
+ public void analyseTable_generic(Long databaseId, Long tableId) throws TableNotFoundException, QueryMalformedException {
+
+ /* mock */
+ when(tableService.suggestTableSemantics(databaseId, tableId))
+ .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) throws QueryMalformedException,
+ TableColumnNotFoundException {
+
+ /* mock */
+ when(tableService.suggestTableColumnSemantics(databaseId, tableId, columnId))
+ .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);
+ }
+}
diff --git a/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/OntologyServiceIntegrationTest.java b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/OntologyServiceIntegrationTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..1dc8023c3d8bcf3499b09df8a5fbadb06535565f
--- /dev/null
+++ b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/OntologyServiceIntegrationTest.java
@@ -0,0 +1,116 @@
+package at.tuwien.service;
+
+import at.tuwien.BaseUnitTest;
+import at.tuwien.entities.semantics.Ontology;
+import at.tuwien.exception.OntologyNotFoundException;
+import at.tuwien.exception.UserNotFoundException;
+import at.tuwien.repository.jpa.OntologyRepository;
+import at.tuwien.repository.jpa.RealmRepository;
+import at.tuwien.repository.jpa.UserRepository;
+import lombok.extern.log4j.Log4j2;
+import org.apache.jena.sys.JenaSystem;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.BeforeEach;
+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.test.annotation.DirtiesContext;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
+
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+
+@Log4j2
+@SpringBootTest
+@DirtiesContext(classMode = DirtiesContext.ClassMode.BEFORE_EACH_TEST_METHOD)
+@ExtendWith(SpringExtension.class)
+public class OntologyServiceIntegrationTest extends BaseUnitTest {
+
+ @Autowired
+ private OntologyService ontologyService;
+
+ @Autowired
+ private UserRepository userRepository;
+
+ @Autowired
+ private RealmRepository realmRepository;
+
+ @Autowired
+ private OntologyRepository ontologyRepository;
+
+ @BeforeAll
+ public static void beforeAll() {
+ JenaSystem.init();
+ }
+
+ @BeforeEach
+ public void beforeEach() {
+ realmRepository.save(REALM_DBREPO);
+ userRepository.save(USER_1);
+ ontologyRepository.save(ONTOLOGY_1);
+ ontologyRepository.save(ONTOLOGY_2);
+ }
+
+ @Test
+ public void findAll_succeeds() {
+
+ /* test */
+ final List<Ontology> response = ontologyService.findAll();
+ assertEquals(2, response.size());
+ }
+
+ @Test
+ public void find_succeeds() throws OntologyNotFoundException {
+
+ /* test */
+ final Ontology response = ontologyService.find(ONTOLOGY_1_ID);
+ assertEquals(ONTOLOGY_1_ID, response.getId());
+ assertEquals(ONTOLOGY_1_URI, response.getUri());
+ }
+
+ @Test
+ public void find_fails() {
+
+ /* test */
+ assertThrows(OntologyNotFoundException.class, () -> {
+ ontologyService.find(9999L);
+ });
+ }
+
+ @Test
+ public void create_succeeds() throws UserNotFoundException {
+
+ /* test */
+ final Ontology response = ontologyService.create(ONTOLOGY_3_CREATE_DTO, USER_1_PRINCIPAL);
+ assertEquals(ONTOLOGY_3_ID, response.getId());
+ assertEquals(ONTOLOGY_3_URI, response.getUri());
+ }
+
+ @Test
+ public void create_notFound_fails() {
+
+ /* test */
+ assertThrows(UserNotFoundException.class, () -> {
+ ontologyService.create(ONTOLOGY_3_CREATE_DTO, USER_3_PRINCIPAL);
+ });
+ }
+
+ @Test
+ public void delete_succeeds() throws OntologyNotFoundException {
+
+ /* test */
+ ontologyService.delete(ONTOLOGY_1_ID);
+ }
+
+ @Test
+ public void delete_fails() {
+
+ /* test */
+ assertThrows(OntologyNotFoundException.class, () -> {
+ ontologyService.delete(9999L);
+ });
+ }
+}
diff --git a/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/QueryServiceUnitTest.java b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/QueryServiceIntegrationTest.java
similarity index 65%
rename from dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/QueryServiceUnitTest.java
rename to dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/QueryServiceIntegrationTest.java
index 0a7ee7eb9144bb4f0bcdee3f8b08ea7d1c030851..42af85f682e383c07469c9ac9f6abdac422ed202 100644
--- a/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/QueryServiceUnitTest.java
+++ b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/QueryServiceIntegrationTest.java
@@ -10,21 +10,23 @@ import lombok.extern.log4j.Log4j2;
import org.apache.jena.sys.JenaSystem;
import org.junit.jupiter.api.BeforeAll;
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.test.annotation.DirtiesContext;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import java.util.List;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.*;
@Log4j2
@SpringBootTest
+@DirtiesContext(classMode = DirtiesContext.ClassMode.BEFORE_EACH_TEST_METHOD)
@ExtendWith(SpringExtension.class)
-public class QueryServiceUnitTest extends BaseUnitTest {
+public class QueryServiceIntegrationTest extends BaseUnitTest {
@Autowired
private RealmRepository realmRepository;
@@ -47,10 +49,7 @@ public class QueryServiceUnitTest extends BaseUnitTest {
public void beforeEach() {
realmRepository.save(REALM_DBREPO);
userRepository.save(USER_1);
- ontologyRepository.save(ONTOLOGY_1);
- ontologyRepository.save(ONTOLOGY_2);
- ontologyRepository.save(ONTOLOGY_3);
- ontologyRepository.save(ONTOLOGY_4);
+ ontologyRepository.saveAll(List.of(ONTOLOGY_1, ONTOLOGY_2, ONTOLOGY_3, ONTOLOGY_4));
}
@Test
@@ -65,15 +64,27 @@ public class QueryServiceUnitTest extends BaseUnitTest {
}
@Test
- public void findByLabel_measurements_succeeds() throws QueryMalformedException {
+ @Disabled
+ public void findByLabel_measurements_fails() throws QueryMalformedException {
/* test */
final List<EntityDto> response = queryService.findByLabel(ONTOLOGY_1, "tonne");
assertEquals(1, response.size());
final EntityDto entity0 = response.get(0);
assertEquals(COLUMN_UNIT_TON_NAME, entity0.getLabel());
- assertEquals(COLUMN_UNIT_TON_URI, entity0.getUri());
- assertEquals(COLUMN_UNIT_TON_DESCRIPTION, entity0.getDescription());
+ assertNull(COLUMN_UNIT_TON_URI);
+ assertNull(COLUMN_UNIT_TON_DESCRIPTION);
+ }
+
+ @Test
+ public void findByLabel_dbpedia_succeeds() throws QueryMalformedException {
+
+ /* test */
+ final List<EntityDto> response = queryService.findByLabel(ONTOLOGY_5, "person");
+ assertTrue(response.size() >= 1);
+ final EntityDto entity0 = response.get(0);
+ assertEquals("person", entity0.getLabel());
+ assertNull(entity0.getDescription());
}
@Test
@@ -97,14 +108,27 @@ public class QueryServiceUnitTest extends BaseUnitTest {
}
@Test
- public void findByUri_measurements_succeeds() throws QueryMalformedException {
+ @Disabled
+ public void findByUri_measurements_fails() throws QueryMalformedException {
/* test */
final List<EntityDto> response = queryService.findByUri(ONTOLOGY_1, COLUMN_UNIT_TON_URI);
assertEquals(1, response.size());
final EntityDto entity0 = response.get(0);
assertEquals(COLUMN_UNIT_TON_URI, entity0.getUri());
- assertEquals(COLUMN_UNIT_TON_NAME, entity0.getLabel());
- assertEquals(COLUMN_UNIT_TON_DESCRIPTION, entity0.getDescription());
+ assertNull(COLUMN_UNIT_TON_NAME);
+ assertNull(COLUMN_UNIT_TON_DESCRIPTION);
+ }
+
+ @Test
+ public void findByUri_dbpedia_fails() throws QueryMalformedException {
+
+ /* test */
+ final List<EntityDto> response = queryService.findByUri(ONTOLOGY_5, "http://dbpedia.org/ontology/person");
+ assertEquals(1, response.size());
+ final EntityDto entity0 = response.get(0);
+ assertEquals("http://dbpedia.org/ontology/person", entity0.getUri());
+ assertEquals("person", entity0.getLabel());
+ assertNull(entity0.getDescription());
}
}
diff --git a/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/SemanticServiceUnitTest.java b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/SemanticServiceUnitTest.java
index 0b997fd6b7d2f65d1c4f68cd03778fde4b2ec67a..ed5171a3327ff929282ee9b5d71c477220a46213 100644
--- a/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/SemanticServiceUnitTest.java
+++ b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/SemanticServiceUnitTest.java
@@ -9,7 +9,6 @@ import org.apache.jena.sys.JenaSystem;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
-import org.mockito.ArgumentMatchers;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.test.mock.mockito.MockBean;
diff --git a/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/TableServiceIntegrationTest.java b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/TableServiceIntegrationTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..c81035a6db938872ba93eb540d3dff5c6b85f6ae
--- /dev/null
+++ b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/TableServiceIntegrationTest.java
@@ -0,0 +1,79 @@
+package at.tuwien.service;
+
+import at.tuwien.BaseUnitTest;
+import at.tuwien.api.semantics.EntityDto;
+import at.tuwien.api.semantics.TableColumnEntityDto;
+import at.tuwien.entities.database.table.columns.TableColumnKey;
+import at.tuwien.exception.QueryMalformedException;
+import at.tuwien.exception.TableColumnNotFoundException;
+import at.tuwien.exception.TableNotFoundException;
+import at.tuwien.repository.jpa.OntologyRepository;
+import at.tuwien.repository.jpa.TableColumnRepository;
+import at.tuwien.repository.jpa.TableRepository;
+import lombok.extern.log4j.Log4j2;
+import org.apache.jena.sys.JenaSystem;
+import org.junit.jupiter.api.BeforeAll;
+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 java.util.Optional;
+
+import static org.junit.jupiter.api.Assertions.*;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.when;
+
+@Log4j2
+@SpringBootTest
+@ExtendWith(SpringExtension.class)
+public class TableServiceIntegrationTest extends BaseUnitTest {
+
+ @Autowired
+ private TableService tableService;
+
+ @MockBean
+ private TableRepository tableRepository;
+
+ @MockBean
+ private OntologyRepository ontologyRepository;
+
+ @MockBean
+ private TableColumnRepository tableColumnRepository;
+
+ @BeforeAll
+ public static void beforeAll() {
+ JenaSystem.init();
+ }
+
+ @Test
+ public void suggestTableSemantics_success() throws TableNotFoundException, QueryMalformedException {
+
+ /* mock */
+ when(tableRepository.findByDatabaseIdAndId(DATABASE_1_ID, TABLE_1_ID))
+ .thenReturn(Optional.of(TABLE_1));
+ when(ontologyRepository.findAll())
+ .thenReturn(List.of(ONTOLOGY_1, ONTOLOGY_2, ONTOLOGY_3, ONTOLOGY_4, ONTOLOGY_5));
+
+ /* test */
+ final List<EntityDto> response = tableService.suggestTableSemantics(DATABASE_1_ID, TABLE_1_ID);
+ assertNotNull(response);
+ }
+
+ @Test
+ public void suggestTableColumnSemantics_success() throws QueryMalformedException, TableColumnNotFoundException {
+
+ /* mock */
+ when(tableColumnRepository.findById(any(TableColumnKey.class)))
+ .thenReturn(Optional.of(TABLE_1_COLUMNS.get(0)));
+ when(ontologyRepository.findAll())
+ .thenReturn(List.of(ONTOLOGY_1, ONTOLOGY_2, ONTOLOGY_3, ONTOLOGY_4, ONTOLOGY_5));
+
+ /* test */
+ final List<TableColumnEntityDto> response = tableService.suggestTableColumnSemantics(DATABASE_1_ID, TABLE_1_ID, COLUMN_1_1_ID);
+ assertNotNull(response);
+ }
+}
diff --git a/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/TableServiceUnitTest.java b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/TableServiceUnitTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..f84d3ea1d96b118a7da4bd468b11bfa4303a6045
--- /dev/null
+++ b/dbrepo-semantics-service/rest-service/src/test/java/at/tuwien/service/TableServiceUnitTest.java
@@ -0,0 +1,63 @@
+package at.tuwien.service;
+
+import at.tuwien.BaseUnitTest;
+import at.tuwien.entities.database.table.Table;
+import at.tuwien.exception.TableNotFoundException;
+import at.tuwien.repository.jpa.TableRepository;
+import lombok.extern.log4j.Log4j2;
+import org.apache.jena.sys.JenaSystem;
+import org.junit.jupiter.api.BeforeAll;
+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.Optional;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.mockito.Mockito.when;
+
+@Log4j2
+@SpringBootTest
+@ExtendWith(SpringExtension.class)
+public class TableServiceUnitTest extends BaseUnitTest {
+
+ @Autowired
+ private TableService tableService;
+
+ @MockBean
+ private TableRepository tableRepository;
+
+ @BeforeAll
+ public static void beforeAll() {
+ JenaSystem.init();
+ }
+
+ @Test
+ public void find_success() throws TableNotFoundException {
+
+ /* mock */
+ when(tableRepository.findByDatabaseIdAndId(DATABASE_1_ID, TABLE_1_ID))
+ .thenReturn(Optional.of(TABLE_1));
+
+ /* test */
+ final Table response = tableService.find(DATABASE_1_ID, TABLE_1_ID);
+ assertEquals(TABLE_1_ID, response.getId());
+ }
+
+ @Test
+ public void find_fails() {
+
+ /* mock */
+ when(tableRepository.findByDatabaseIdAndId(DATABASE_1_ID, TABLE_1_ID))
+ .thenReturn(Optional.empty());
+
+ /* test */
+ assertThrows(TableNotFoundException.class, () -> {
+ tableService.find(DATABASE_1_ID, TABLE_1_ID);
+ });
+ }
+}
diff --git a/dbrepo-semantics-service/services/src/main/java/at/tuwien/exception/UserNotFoundException.java b/dbrepo-semantics-service/services/src/main/java/at/tuwien/exception/UserNotFoundException.java
new file mode 100644
index 0000000000000000000000000000000000000000..f758f7ddf3b3a9d28b2bfc7584a829e41d7c125f
--- /dev/null
+++ b/dbrepo-semantics-service/services/src/main/java/at/tuwien/exception/UserNotFoundException.java
@@ -0,0 +1,21 @@
+package at.tuwien.exception;
+
+import org.springframework.http.HttpStatus;
+import org.springframework.web.bind.annotation.ResponseStatus;
+
+@ResponseStatus(code = HttpStatus.NOT_FOUND)
+public class UserNotFoundException extends Exception {
+
+ public UserNotFoundException(String msg) {
+ super(msg);
+ }
+
+ public UserNotFoundException(String msg, Throwable thr) {
+ super(msg, thr);
+ }
+
+ public UserNotFoundException(Throwable thr) {
+ super(thr);
+ }
+
+}
diff --git a/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/OntologyService.java b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/OntologyService.java
index f903a67428090f455ca6c1e5e9434445cf69c943..4a55f52491007c5ecae69bc6c59698541284a528 100644
--- a/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/OntologyService.java
+++ b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/OntologyService.java
@@ -4,7 +4,9 @@ import at.tuwien.api.semantics.OntologyCreateDto;
import at.tuwien.api.semantics.OntologyModifyDto;
import at.tuwien.entities.semantics.Ontology;
import at.tuwien.exception.OntologyNotFoundException;
+import at.tuwien.exception.UserNotFoundException;
+import java.security.Principal;
import java.util.List;
public interface OntologyService {
@@ -12,7 +14,7 @@ public interface OntologyService {
Ontology find(Long id) throws OntologyNotFoundException;
- Ontology create(OntologyCreateDto data);
+ Ontology create(OntologyCreateDto data, Principal principal) throws UserNotFoundException;
Ontology update(Long id, OntologyModifyDto data) throws OntologyNotFoundException;
diff --git a/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/UserService.java b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/UserService.java
new file mode 100644
index 0000000000000000000000000000000000000000..6de26b3ffc045f5b7c4ac19223581e0f73a98b86
--- /dev/null
+++ b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/UserService.java
@@ -0,0 +1,8 @@
+package at.tuwien.service;
+
+import at.tuwien.entities.user.User;
+import at.tuwien.exception.UserNotFoundException;
+
+public interface UserService {
+ User findByUsername(String username) throws UserNotFoundException;
+}
diff --git a/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/OntologyServiceImpl.java b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/OntologyServiceImpl.java
index 591538373140e9cacf00d5926e10daef58626520..5137f9f92d234d32b3f905fa634b13a68777c7a0 100644
--- a/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/OntologyServiceImpl.java
+++ b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/OntologyServiceImpl.java
@@ -3,14 +3,18 @@ package at.tuwien.service.impl;
import at.tuwien.api.semantics.OntologyCreateDto;
import at.tuwien.api.semantics.OntologyModifyDto;
import at.tuwien.entities.semantics.Ontology;
+import at.tuwien.entities.user.User;
import at.tuwien.exception.OntologyNotFoundException;
+import at.tuwien.exception.UserNotFoundException;
import at.tuwien.mapper.OntologyMapper;
import at.tuwien.repository.jpa.OntologyRepository;
import at.tuwien.service.OntologyService;
+import at.tuwien.service.UserService;
import lombok.extern.log4j.Log4j2;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
+import java.security.Principal;
import java.util.List;
import java.util.Optional;
@@ -18,11 +22,14 @@ import java.util.Optional;
@Service
public class OntologyServiceImpl implements OntologyService {
+ private final UserService userService;
private final OntologyMapper ontologyMapper;
private final OntologyRepository ontologyRepository;
@Autowired
- public OntologyServiceImpl(OntologyMapper ontologyMapper, OntologyRepository ontologyRepository) {
+ public OntologyServiceImpl(UserService userService, OntologyMapper ontologyMapper,
+ OntologyRepository ontologyRepository) {
+ this.userService = userService;
this.ontologyMapper = ontologyMapper;
this.ontologyRepository = ontologyRepository;
}
@@ -43,8 +50,11 @@ public class OntologyServiceImpl implements OntologyService {
}
@Override
- public Ontology create(OntologyCreateDto data) {
- final Ontology ontology = ontologyRepository.save(ontologyMapper.ontologyCreateDtoToOntology(data));
+ public Ontology create(OntologyCreateDto data, Principal principal) throws UserNotFoundException {
+ final User user = userService.findByUsername(principal.getName());
+ final Ontology entity = ontologyMapper.ontologyCreateDtoToOntology(data);
+ entity.setCreatedBy(user.getId());
+ final Ontology ontology = ontologyRepository.save(entity);
log.info("Created ontology with id {}", ontology.getId());
return ontology;
}
diff --git a/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/QueryServiceImpl.java b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/QueryServiceImpl.java
index 5b51cfdf8c7457b38c748d4b955516a5e51e1740..742c2090371ede84aa77b90e3dd00c862388bd4c 100644
--- a/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/QueryServiceImpl.java
+++ b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/QueryServiceImpl.java
@@ -7,22 +7,15 @@ import at.tuwien.mapper.OntologyMapper;
import at.tuwien.repository.jpa.OntologyRepository;
import at.tuwien.service.QueryService;
import lombok.extern.log4j.Log4j2;
-import org.apache.jena.graph.Node;
-import org.apache.jena.graph.NodeFactory;
import org.apache.jena.query.*;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.riot.RiotException;
-import org.apache.jena.sparql.algebra.op.OpService;
-import org.apache.jena.sparql.service.ServiceExecutorRegistry;
-import org.apache.jena.sparql.service.single.ChainingServiceExecutor;
-import org.apache.jena.sparql.util.Context;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
-import java.util.Objects;
@Log4j2
@Service
@@ -33,29 +26,10 @@ public class QueryServiceImpl implements QueryService {
private final OntologyRepository ontologyRepository;
@Autowired
- public QueryServiceImpl(OntologyRepository ontologyRepository, OntologyMapper ontologyMapper,
- OntologyRepository ontologyRepository1) {
+ public QueryServiceImpl(OntologyRepository ontologyRepository, OntologyMapper ontologyMapper) {
this.ontologyMapper = ontologyMapper;
- this.ontologyRepository = ontologyRepository1;
- final Context context = ARQ.getContext().copy();
+ this.ontologyRepository = ontologyRepository;
this.dataset = DatasetFactory.create();
- /* registry */
- final ServiceExecutorRegistry registry = ServiceExecutorRegistry.get(context).copy();
- ontologyRepository.findAll()
- .stream()
- .filter(o -> Objects.nonNull(o.getSparqlEndpoint()))
- .forEach(ontology -> {
- final Node node = NodeFactory.createURI(ontology.getSparqlEndpoint());
- ChainingServiceExecutor relaySef = (opExecute, original, binding, execCxt, chain) -> {
- if (opExecute.getService().equals(node)) {
- opExecute = new OpService(node, opExecute.getSubOp(), opExecute.getSilent());
- }
- return chain.createExecution(opExecute, original, binding, execCxt);
- };
- log.debug("add sparql endpoint {}", ontology.getSparqlEndpoint());
- registry.addSingleLink(relaySef);
- });
- ServiceExecutorRegistry.set(context, registry);
}
@Override
diff --git a/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/UserServiceImpl.java b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/UserServiceImpl.java
new file mode 100644
index 0000000000000000000000000000000000000000..99bc7ae5d4b79169e3864397427310ef9e78ffab
--- /dev/null
+++ b/dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/UserServiceImpl.java
@@ -0,0 +1,34 @@
+package at.tuwien.service.impl;
+
+import at.tuwien.entities.user.User;
+import at.tuwien.exception.UserNotFoundException;
+import at.tuwien.repository.jpa.UserRepository;
+import at.tuwien.service.UserService;
+import lombok.extern.log4j.Log4j2;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import java.util.Optional;
+
+@Log4j2
+@Service
+public class UserServiceImpl implements UserService {
+
+ private final UserRepository userRepository;
+
+ @Autowired
+ public UserServiceImpl(UserRepository userRepository) {
+ this.userRepository = userRepository;
+ }
+
+ @Override
+ public User findByUsername(String username) throws UserNotFoundException {
+ final Optional<User> optional = userRepository.findByUsername(username);
+ if (optional.isEmpty()) {
+ log.error("Failed to find user with username {}", username);
+ throw new UserNotFoundException("Failed to find user with username " + username);
+ }
+ return optional.get();
+ }
+
+}
diff --git a/dbrepo-ui/components/dialogs/Semantics.vue b/dbrepo-ui/components/dialogs/Semantics.vue
index caf59080020368b8c0989eaa9874ed42169d901c..12f5457002c7369bd6e2526658bf654b5b683692 100644
--- a/dbrepo-ui/components/dialogs/Semantics.vue
+++ b/dbrepo-ui/components/dialogs/Semantics.vue
@@ -16,13 +16,15 @@
icon="mdi-share-variant"
class="pl-6">
<p>
- The following ontologies automatically will query the fields <code>rdfs:label</code> and
- <code>schema:description</code> and store it for this column. You can still use other URIs that are not
- matching these ontologies, the URI will be displayed instead.
+ The following ontologies automatically will query the fields <code>rdfs:label</code> and store it for this
+ column. You can still use other URIs that are not matching these ontologies, the URI will be displayed
+ instead.
</p>
- <div v-for="(item,idx) in ontologies" :key="idx">
- <a :href="item.uri" target="_blank" v-text="item.uri" />
- </div>
+ <ul>
+ <li v-for="(item,idx) in ontologies" :key="idx">
+ <a :href="item.uri" target="_blank" v-text="item.uri" />
+ </li>
+ </ul>
</v-alert>
<v-alert
v-if="entity"
@@ -60,10 +62,12 @@
<v-text-field
v-model="uri"
:loading="loading"
+ :success="canAutomaticResolve"
+ :hint="canAutomaticResolve ? 'This URI can be automatically resolved!' : 'e.g. http://www.wikidata.org/entity/Q468777'"
+ :persistent-hint="canAutomaticResolve"
clearable
label="URI"
:rules="[v => isUri(v) || $t('Must start with http:// or https://')]"
- hint="e.g. http://www.wikidata.org/entity/Q468777"
@click:clear="uri = null" />
</v-col>
</v-row>
@@ -128,7 +132,23 @@ export default {
},
computed: {
ontologies () {
- return this.$store.state.ontologies
+ const ontologies = this.$store.state.ontologies
+ if (!ontologies) {
+ return []
+ }
+ return ontologies.filter(o => o.sparql)
+ },
+ canAutomaticResolve () {
+ if (!this.uri) {
+ return false
+ }
+ let found = false
+ this.ontologies.forEach((o) => {
+ if (this.uri.startsWith(o.uri)) {
+ found = true
+ }
+ })
+ return found
},
entity () {
if (!this.column[this.mode]) {
diff --git a/dbrepo-ui/layouts/default.vue b/dbrepo-ui/layouts/default.vue
index 30596e71b7a544decbfacd93c71eb9d1cb10587a..44edd4a29c34e41e304c0c5f0c319222ddac6b68 100644
--- a/dbrepo-ui/layouts/default.vue
+++ b/dbrepo-ui/layouts/default.vue
@@ -239,7 +239,6 @@ export default {
},
mounted () {
this.$store.dispatch('reloadMessages')
- this.$store.dispatch('reloadOntologies')
if (this.locale) {
this.$i18n.locale = this.locale
}
diff --git a/dbrepo-ui/pages/container/_container_id/database/_database_id/table/_table_id/schema.vue b/dbrepo-ui/pages/container/_container_id/database/_database_id/table/_table_id/schema.vue
index d5c3d1b0778113e068d10088f25c87bce469a702..54d91815591affdff3feea672bc6a1d478725dbb 100644
--- a/dbrepo-ui/pages/container/_container_id/database/_database_id/table/_table_id/schema.vue
+++ b/dbrepo-ui/pages/container/_container_id/database/_database_id/table/_table_id/schema.vue
@@ -168,6 +168,7 @@ export default {
}
},
mounted () {
+ this.$store.dispatch('reloadOntologies')
},
methods: {
isUnique (column) {