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Merge pull request #51 from DiSSCo/bug-fix/fix-table-names
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Fix table name and run auto-format
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@samleeflang
samleeflang authored Dec 12, 2023
2 parents f8b6d4c + da16395 commit 463b7f4
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Showing 10 changed files with 43 additions and 42 deletions.
4 changes: 2 additions & 2 deletions src/main/java/eu/dissco/core/translator/service/DwcaService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -361,8 +361,8 @@ private String getTableName(ArchiveFile archiveFile) {
var fullSourceSystemId = webClientProperties.getSourceSystemId();
var minifiedSourceSystemId = fullSourceSystemId.substring(fullSourceSystemId.indexOf('/') + 1)
.replace("-", "_");
var tableName = (minifiedSourceSystemId + "_" + archiveFile.getRowType()
.prefixedName()).toLowerCase()
var tableName = "temp_" + (minifiedSourceSystemId + "_" + archiveFile.getRowType()
.simpleName()).toLowerCase()
.replace(":", "_");
tableName = tableName.replace("/", "_");
return tableName.replace(".", "_");
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2 changes: 0 additions & 2 deletions src/test/java/eu/dissco/core/translator/component/InstitutionNameComponentTest.java
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Expand Up @@ -2,7 +2,6 @@

import static eu.dissco.core.translator.TestUtils.loadResourceFile;
import static org.assertj.core.api.Assertions.assertThat;
import static org.assertj.core.api.Assertions.assertThatThrownBy;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyString;
Expand All @@ -11,7 +10,6 @@
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dissco.core.translator.exception.OrganisationException;
import java.io.IOException;
import java.util.concurrent.CompletableFuture;
import java.util.concurrent.ExecutionException;
import org.junit.jupiter.api.BeforeEach;
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36 changes: 18 additions & 18 deletions src/test/java/eu/dissco/core/translator/repository/BatchInserterTest.java
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Expand Up @@ -24,16 +24,28 @@
import org.junit.jupiter.params.provider.MethodSource;
import org.postgresql.copy.CopyManager;
import org.postgresql.core.BaseConnection;
import org.testcontainers.shaded.org.yaml.snakeyaml.events.Event.ID;

class BatchInserterTest extends BaseRepositoryIT {

private BatchInserter batchInserter;
private static final String TABLE_NAME = "xxx_xxx_xxx_core";
private final Field<String> ID_FIELD = DSL.field("dwcaid", String.class);
private static final String TABLE_NAME = "temp_xxx_xxx_xxx_core";
private static final Field<JSONB> DATA_FIELD = DSL.field("data", JSONB.class);
private static final String RECORD_ID = "11a8a4c6-3188-4305-9688-d68942f4038e";
private static final String RECORD_ID_ALT = "32546f7b-f62a-4368-8c60-922f1cba4ab8";
private final Field<String> ID_FIELD = DSL.field("dwcaid", String.class);
private BatchInserter batchInserter;

private static Stream<Arguments> badStrings() {
return Stream.of(
Arguments.of("bad \b string"),
Arguments.of("bad \f string"),
Arguments.of("bad \n string"),
Arguments.of("bad \r string"),
Arguments.of("bad \t string"),
Arguments.of("bad, string"),
Arguments.of("bad \\N string")
);
}

@BeforeEach
void setup() throws SQLException {
var connection = DriverManager.getConnection(dataSource.getJdbcUrl(), dataSource.getUsername(),
Expand All @@ -48,7 +60,7 @@ void setup() throws SQLException {
}

@AfterEach
void destroy(){
void destroy() {
context.dropTableIfExists(getTable(TABLE_NAME)).execute();
}

Expand Down Expand Up @@ -113,26 +125,14 @@ void testBadCharacters() throws Exception {
assertThat(MAPPER.readTree(result.get(DATA_FIELD).data())).isEqualTo(expected);
}

private static Stream<Arguments> badStrings(){
return Stream.of(
Arguments.of("bad \b string"),
Arguments.of("bad \f string"),
Arguments.of("bad \n string"),
Arguments.of("bad \r string"),
Arguments.of("bad \t string"),
Arguments.of("bad, string"),
Arguments.of("bad \\N string")
);
}

private List<Pair<String, JsonNode>> givenCoreRecords() {
var records = new ArrayList<Pair<String, JsonNode>>();
records.add(Pair.of(RECORD_ID, givenJsonNode()));
records.add(Pair.of(RECORD_ID_ALT, MAPPER.createObjectNode()));
return records;
}

private JsonNode givenJsonNode(){
private JsonNode givenJsonNode() {
var node = MAPPER.createObjectNode();
node.put("test", "test");
node.put("data", "value");
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15 changes: 7 additions & 8 deletions src/test/java/eu/dissco/core/translator/repository/DwcaRepositoryTest.java
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Expand Up @@ -30,12 +30,11 @@
@ExtendWith(MockitoExtension.class)
class DwcaRepositoryTest extends BaseRepositoryIT {

private DwcaRepository repository;
@Mock
BatchInserter batchInserter;

private final Field<String> idField = DSL.field("dwcaid", String.class);
private final Field<JSONB> dataField = DSL.field("data", JSONB.class);
@Mock
BatchInserter batchInserter;
private DwcaRepository repository;

private static JsonNode givenRecord(String corruptedValue) {
var objectNode = MAPPER.createObjectNode();
Expand All @@ -52,7 +51,7 @@ void setup() {
@Test
void getCoreRecords() {
// Given
var tableName = "XXX-XXX-XXX_Core";
var tableName = "temp_XXX-XXX-XXX_Core";
var records = givenCoreRecords();
repository.createTable(tableName);
postRecords(tableName, records);
Expand All @@ -70,7 +69,7 @@ void getCoreRecords() {
@Test
void getCorruptCoreRecords() {
// Given
var tableName = "XXX-XXX-XXX_Core";
var tableName = "temp_XXX-XXX-XXX_Core";
var records = List.of(
Pair.of(UUID.randomUUID().toString(), givenRecord("\u0000 someCorruptedInformation")));
repository.createTable(tableName);
Expand All @@ -89,7 +88,7 @@ void getCorruptCoreRecords() {
@Test
void getCoreExtensionRecords() {
// Given
var tableName = "XXX-XXX-XXX_Extension";
var tableName = "temp_XXX-XXX-XXX_Extension";
var records = givenExtensionRecord();
repository.createTable(tableName);
postRecords(tableName, records);
Expand All @@ -106,7 +105,7 @@ void getCoreExtensionRecords() {
@Test
void testPostRecords() throws Exception {
// Given
var tableName = "XXX-XXX-XXX_Extension";
var tableName = "temp_XXX-XXX-XXX_Extension";
var records = givenExtensionRecord();

// When
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11 changes: 6 additions & 5 deletions src/test/java/eu/dissco/core/translator/service/DwcaServiceTest.java
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Expand Up @@ -132,7 +132,7 @@ void testCopyTableFails() throws Exception {
// Given
givenDWCA("/dwca-rbins.zip");
doThrow(new DisscoRepositoryException("", new Exception())).when(dwcaRepository)
.postRecords(eq("abc_ddd_asd_dwc_occurrence"), anyList());
.postRecords(eq("temp_abc_ddd_asd_occurrence"), anyList());

// When
service.retrieveData();
Expand Down Expand Up @@ -229,9 +229,9 @@ void testRetrieveDataWithGbifMedia() throws Exception {
// Given
givenDWCA("/dwca-kew-gbif-media.zip");
given(dwcaRepository.getCoreRecords(anyList(), anyString())).willReturn(givenSpecimenMap(19));
given(dwcaRepository.getRecords(anyList(), eq("abc_ddd_asd_dwc_identification"))).willReturn(
given(dwcaRepository.getRecords(anyList(), eq("temp_abc_ddd_asd_identification"))).willReturn(
Map.of());
given(dwcaRepository.getRecords(anyList(), eq("abc_ddd_asd_gbif_multimedia"))).willReturn(
given(dwcaRepository.getRecords(anyList(), eq("temp_abc_ddd_asd_multimedia"))).willReturn(
givenImageMap(19));
given(digitalSpecimenDirector.assembleDigitalSpecimenTerm(any(JsonNode.class), anyBoolean()))
.willReturn(givenDigitalSpecimen());
Expand Down Expand Up @@ -267,7 +267,8 @@ void testRetrieveDataWithAcMedia() throws Exception {
// Given
givenDWCA("/dwca-naturalis-ac-media.zip");
given(dwcaRepository.getCoreRecords(anyList(), anyString())).willReturn(givenSpecimenMap(14));
given(dwcaRepository.getRecords(anyList(), eq("abc_ddd_asd_http___rs_tdwg_org_ac_terms_multimedia"))).willReturn(givenImageMap(14));
given(dwcaRepository.getRecords(anyList(),
eq("temp_abc_ddd_asd_multimedia"))).willReturn(givenImageMap(14));
given(digitalSpecimenDirector.assembleDigitalSpecimenTerm(any(JsonNode.class), anyBoolean()))
.willReturn(givenDigitalSpecimen());
given(digitalSpecimenDirector.assembleDigitalMediaObjects(anyBoolean(), any(JsonNode.class),
Expand All @@ -292,7 +293,7 @@ void testRetrieveDataWithInvalidAcMedia() throws Exception {
givenDWCA("/dwca-invalid-ac-media.zip");
given(dwcaRepository.getCoreRecords(anyList(), anyString())).willReturn(givenSpecimenMap(1));
given(dwcaRepository.getRecords(anyList(),
eq("abc_ddd_asd_http___rs_tdwg_org_ac_terms_multimedia"))).willReturn(givenImageMap(1));
eq("temp_abc_ddd_asd_multimedia"))).willReturn(givenImageMap(1));
given(digitalSpecimenDirector.assembleDigitalSpecimenTerm(any(JsonNode.class), anyBoolean()))
.willReturn(givenDigitalSpecimen());
given(digitalSpecimenDirector.assembleDigitalMediaObjects(anyBoolean(), any(JsonNode.class),
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3 changes: 2 additions & 1 deletion src/test/java/eu/dissco/core/translator/service/KafkaServiceTest.java
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Expand Up @@ -48,7 +48,8 @@ void testSendMessage() throws JsonProcessingException {
service.sendMessage("test-topic", digitalSpecimenEvent);

// Then
then(kafkaTemplate).should().send("test-topic", MAPPER.writeValueAsString(digitalSpecimenEvent));
then(kafkaTemplate).should()
.send("test-topic", MAPPER.writeValueAsString(digitalSpecimenEvent));
}

private DigitalSpecimenEvent givenDigitalSpecimenEvent() {
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3 changes: 2 additions & 1 deletion src/test/java/eu/dissco/core/translator/terms/BiocaseDigitalObjectDirectorTest.java
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Expand Up @@ -51,7 +51,8 @@ void setup() {
void testConstructAbcdDigitalSpecimen() throws Exception {
// Given
var specimenJson = givenAbcdSpecimenJson();
given(institutionNameComponent.getWikiDataName(anyString())).willReturn("Tallinn University of Technology");
given(institutionNameComponent.getWikiDataName(anyString())).willReturn(
"Tallinn University of Technology");
given(termMapper.retrieveTerm(any(Term.class), eq(specimenJson), eq(false))).willReturn(
"a mapped term");
given(termMapper.retrieveTerm(any(OrganisationId.class), eq(specimenJson), eq(false)))
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9 changes: 6 additions & 3 deletions src/test/java/eu/dissco/core/translator/terms/DwcaDigitalObjectDirectorTest.java
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Expand Up @@ -38,15 +38,17 @@ class DwcaDigitalObjectDirectorTest {

@BeforeEach
void setup() {
director = new DwcaDigitalObjectDirector(MAPPER, termMapper, institutionNameComponent, webClientProperties,
director = new DwcaDigitalObjectDirector(MAPPER, termMapper, institutionNameComponent,
webClientProperties,
fdoProperties);
}

@Test
void testConstructDwcaDigitalSpecimen() throws Exception {
// Given
var specimenJson = givenDwcaSpecimenJson();
given(institutionNameComponent.getRorName(anyString())).willReturn("National Museum of Natural History");
given(institutionNameComponent.getRorName(anyString())).willReturn(
"National Museum of Natural History");
given(termMapper.retrieveTerm(any(Term.class), eq(specimenJson), eq(true))).willReturn(
"a mapped term");
given(termMapper.retrieveTerm(any(OrganisationId.class), eq(specimenJson), eq(true)))
Expand All @@ -69,7 +71,8 @@ void testConstructDwcaDigitalSpecimen() throws Exception {
void testConstructDwcaDigitalMediaObject() throws JsonProcessingException, OrganisationException {
// Given
var specimenJson = givenDwcaMediaObject();
given(institutionNameComponent.getRorName(anyString())).willReturn("National Museum of Natural History");
given(institutionNameComponent.getRorName(anyString())).willReturn(
"National Museum of Natural History");
given(termMapper.retrieveTerm(any(Term.class), eq(specimenJson), eq(true))).willReturn(
"a mapped term");

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1 change: 0 additions & 1 deletion src/test/java/eu/dissco/core/translator/terms/specimen/DataGeneralizationsTest.java
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Expand Up @@ -3,7 +3,6 @@
import static eu.dissco.core.translator.TestUtils.MAPPER;
import static org.assertj.core.api.Assertions.assertThat;

import eu.dissco.core.translator.terms.specimen.DataGeneralizations;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.junit.jupiter.MockitoExtension;
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1 change: 0 additions & 1 deletion src/test/java/eu/dissco/core/translator/terms/specimen/InformationWithheldTest.java
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Expand Up @@ -3,7 +3,6 @@
import static eu.dissco.core.translator.TestUtils.MAPPER;
import static org.assertj.core.api.Assertions.assertThat;

import eu.dissco.core.translator.terms.specimen.InformationWithheld;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.junit.jupiter.MockitoExtension;
Expand Down

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