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Merge pull request #50 from DiSSCo/feature/pgcopy-temp-tables
Copy batches into db
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26
src/main/java/eu/dissco/core/translator/configuration/BatchInserterConfig.java
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| package eu.dissco.core.translator.configuration; | ||
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| import java.sql.DriverManager; | ||
| import java.sql.SQLException; | ||
| import lombok.RequiredArgsConstructor; | ||
| import org.springframework.boot.autoconfigure.jdbc.DataSourceProperties; | ||
| import org.springframework.context.annotation.Configuration; | ||
| import org.postgresql.copy.CopyManager; | ||
| import org.postgresql.core.BaseConnection; | ||
| import org.springframework.context.annotation.Bean; | ||
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| @Configuration | ||
| @RequiredArgsConstructor | ||
| public class BatchInserterConfig { | ||
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| private final DataSourceProperties properties; | ||
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| @Bean | ||
| public CopyManager copyManager() throws SQLException { | ||
| var connection = DriverManager.getConnection(properties.getUrl(), properties.getUsername(), | ||
| properties.getPassword()); | ||
| return new CopyManager((BaseConnection) connection); | ||
| } | ||
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| } |
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57 changes: 57 additions & 0 deletions
57
src/main/java/eu/dissco/core/translator/repository/BatchInserter.java
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| Original file line number | Diff line number | Diff line change |
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| package eu.dissco.core.translator.repository; | ||
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| import com.fasterxml.jackson.databind.JsonNode; | ||
| import eu.dissco.core.translator.exception.DisscoRepositoryException; | ||
| import java.io.ByteArrayInputStream; | ||
| import java.io.ByteArrayOutputStream; | ||
| import java.io.IOException; | ||
| import java.nio.charset.StandardCharsets; | ||
| import java.sql.SQLException; | ||
| import java.util.List; | ||
| import lombok.RequiredArgsConstructor; | ||
| import lombok.extern.slf4j.Slf4j; | ||
| import org.apache.commons.lang3.tuple.Pair; | ||
| import org.postgresql.copy.CopyManager; | ||
| import org.springframework.stereotype.Component; | ||
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| @Component | ||
| @RequiredArgsConstructor | ||
| @Slf4j | ||
| public class BatchInserter { | ||
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| private final CopyManager copyManager; | ||
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| public void batchCopy(String tableName, List<Pair<String, JsonNode>> dbRecords) | ||
| throws DisscoRepositoryException { | ||
| try (var outputStream = new ByteArrayOutputStream()) { | ||
| for (var dbRecord : dbRecords) { | ||
| outputStream.write(getCsvRow(dbRecord)); | ||
| } | ||
| var inputStream = new ByteArrayInputStream(outputStream.toByteArray()); | ||
| copyManager.copyIn("COPY " + tableName | ||
| + " FROM stdin DELIMITER ','", inputStream); | ||
| } catch (IOException | SQLException e) { | ||
| throw new DisscoRepositoryException( | ||
| String.format("An error has occurred inserting %d records into temp table %s", | ||
| dbRecords.size(), tableName), e); | ||
| } | ||
| } | ||
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| private static byte[] getCsvRow(Pair<String, JsonNode> dbRecord) { | ||
| return (dbRecord.getLeft() + "," + | ||
| cleanString(dbRecord.getRight()) | ||
| + "\n").getBytes(StandardCharsets.UTF_8); | ||
| } | ||
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| private static String cleanString(JsonNode jsonNode) { | ||
| if (jsonNode.isEmpty()) { | ||
| return "{}"; | ||
| } | ||
| var node = jsonNode.toString(); | ||
| node = node.replace("\\u0000", ""); | ||
| node = node.replace("\\", "\\\\"); | ||
| node = node.replace(",", "\\,"); | ||
| return node; | ||
| } | ||
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| } |
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145 changes: 145 additions & 0 deletions
145
src/test/java/eu/dissco/core/translator/repository/BatchInserterTest.java
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| Original file line number | Diff line number | Diff line change |
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| package eu.dissco.core.translator.repository; | ||
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| import static eu.dissco.core.translator.TestUtils.MAPPER; | ||
| import static org.assertj.core.api.Assertions.assertThat; | ||
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| import com.fasterxml.jackson.databind.JsonNode; | ||
| import java.sql.DriverManager; | ||
| import java.sql.SQLException; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.stream.Stream; | ||
| import org.apache.commons.lang3.tuple.Pair; | ||
| import org.jooq.Field; | ||
| import org.jooq.JSONB; | ||
| import org.jooq.Record; | ||
| import org.jooq.Table; | ||
| import org.jooq.impl.DSL; | ||
| import org.jooq.impl.SQLDataType; | ||
| import org.junit.jupiter.api.AfterEach; | ||
| import org.junit.jupiter.api.BeforeEach; | ||
| import org.junit.jupiter.api.Test; | ||
| import org.junit.jupiter.params.ParameterizedTest; | ||
| import org.junit.jupiter.params.provider.Arguments; | ||
| 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; | ||
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| class BatchInserterTest extends BaseRepositoryIT { | ||
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| 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 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"; | ||
| @BeforeEach | ||
| void setup() throws SQLException { | ||
| var connection = DriverManager.getConnection(dataSource.getJdbcUrl(), dataSource.getUsername(), | ||
| dataSource.getPassword()); | ||
| var copyManager = new CopyManager((BaseConnection) connection); | ||
| batchInserter = new BatchInserter(copyManager); | ||
| context.createTable(TABLE_NAME) | ||
| .column(ID_FIELD, SQLDataType.VARCHAR) | ||
| .column(DATA_FIELD, SQLDataType.JSONB) | ||
| .execute(); | ||
| context.createIndex().on(TABLE_NAME, ID_FIELD.getName()).execute(); | ||
| } | ||
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| @AfterEach | ||
| void destroy(){ | ||
| context.dropTableIfExists(getTable(TABLE_NAME)).execute(); | ||
| } | ||
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| @Test | ||
| void testBatchInsert() throws Exception { | ||
| // Given | ||
| var records = givenCoreRecords(); | ||
| var idField = context.meta().getTables(TABLE_NAME).get(0).field(ID_FIELD); | ||
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| // When | ||
| batchInserter.batchCopy(TABLE_NAME, records); | ||
| var result = context.select(getTable(TABLE_NAME).asterisk()) | ||
| .from(getTable(TABLE_NAME)) | ||
| .where(idField.eq(RECORD_ID)) | ||
| .fetchOne(); | ||
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| // Then | ||
| assertThat(MAPPER.readTree(result.get(DATA_FIELD).data())).isEqualTo(givenJsonNode()); | ||
| } | ||
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| @ParameterizedTest | ||
| @MethodSource("badStrings") | ||
| void testBadCharacters(String badString) throws Exception { | ||
| // Given | ||
| var node = MAPPER.createObjectNode(); | ||
| node.put("field", badString); | ||
| var pair = List.of(Pair.of(RECORD_ID, (JsonNode) node)); | ||
| var idField = context.meta().getTables(TABLE_NAME).get(0).field(ID_FIELD); | ||
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| // When | ||
| batchInserter.batchCopy(TABLE_NAME, pair); | ||
| var result = context.select(getTable(TABLE_NAME).asterisk()) | ||
| .from(getTable(TABLE_NAME)) | ||
| .where(idField.eq(RECORD_ID)) | ||
| .fetchOne(); | ||
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| // Then | ||
| assertThat(MAPPER.readTree(result.get(DATA_FIELD).data())).isEqualTo(node); | ||
| } | ||
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| @Test | ||
| void testBadCharacters() throws Exception { | ||
| // Given | ||
| var node = MAPPER.createObjectNode(); | ||
| node.put("field", "\u0000"); | ||
| var pair = List.of(Pair.of(RECORD_ID, (JsonNode) node)); | ||
| var expected = MAPPER.readTree(""" | ||
| { | ||
| "field":"" | ||
| } | ||
| """); | ||
| var idField = context.meta().getTables(TABLE_NAME).get(0).field(ID_FIELD); | ||
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| // When | ||
| batchInserter.batchCopy(TABLE_NAME, pair); | ||
| var result = context.select(getTable(TABLE_NAME).asterisk()) | ||
| .from(getTable(TABLE_NAME)) | ||
| .where(idField.eq(RECORD_ID)) | ||
| .fetchOne(); | ||
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| // Then | ||
| assertThat(MAPPER.readTree(result.get(DATA_FIELD).data())).isEqualTo(expected); | ||
| } | ||
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| 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") | ||
| ); | ||
| } | ||
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| 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; | ||
| } | ||
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| private JsonNode givenJsonNode(){ | ||
| var node = MAPPER.createObjectNode(); | ||
| node.put("test", "test"); | ||
| node.put("data", "value"); | ||
| return node; | ||
| } | ||
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| private Table<Record> getTable(String tableName) { | ||
| return DSL.table("\"" + tableName + "\""); | ||
| } | ||
| } |
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