package eu.dnetlib.dhp.collection; import static eu.dnetlib.dhp.common.Constants.MDSTORE_DATA_PATH; import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertNotNull; import java.io.File; import java.io.FileOutputStream; import java.io.FileReader; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.Map; import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.io.IntWritable; import org.apache.hadoop.io.Text; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.*; import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.junit.jupiter.MockitoExtension; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest; import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion; import eu.dnetlib.dhp.schema.mdstore.MetadataRecord; import eu.dnetlib.dhp.schema.mdstore.Provenance; import eu.dnetlib.dhp.transformation.TransformSparkJobNode; @TestMethodOrder(MethodOrderer.OrderAnnotation.class) @ExtendWith(MockitoExtension.class) public class GenerateNativeStoreSparkJobTest extends AbstractVocabularyTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static SparkSession spark; private static Path workingDir; private static Encoder encoder; private static final String encoding = "XML"; private static final String dateOfCollection = System.currentTimeMillis() + ""; private static final String xpath = "//*[local-name()='header']/*[local-name()='identifier']"; private static String provenance; private static final Logger log = LoggerFactory.getLogger(GenerateNativeStoreSparkJobTest.class); @BeforeAll public static void beforeAll() throws IOException { provenance = IOUtils .toString( GenerateNativeStoreSparkJobTest.class .getResourceAsStream("/eu/dnetlib/dhp/collection/provenance.json")); workingDir = Files.createTempDirectory(GenerateNativeStoreSparkJobTest.class.getSimpleName()); log.info("using work dir {}", workingDir); SparkConf conf = new SparkConf(); conf.setAppName(GenerateNativeStoreSparkJobTest.class.getSimpleName()); conf.setMaster("local[*]"); conf.set("spark.driver.host", "localhost"); conf.set("hive.metastore.local", "true"); conf.set("spark.ui.enabled", "false"); conf.set("spark.sql.warehouse.dir", workingDir.toString()); conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); encoder = Encoders.bean(MetadataRecord.class); spark = SparkSession .builder() .appName(GenerateNativeStoreSparkJobTest.class.getSimpleName()) .config(conf) .getOrCreate(); } @AfterAll public static void afterAll() throws IOException { FileUtils.deleteDirectory(workingDir.toFile()); spark.stop(); } @Test @Order(1) void testGenerateNativeStoreSparkJobRefresh() throws Exception { MDStoreVersion mdStoreV1 = prepareVersion("/eu/dnetlib/dhp/collection/mdStoreVersion_1.json"); FileUtils.forceMkdir(new File(mdStoreV1.getHdfsPath())); IOUtils .copy( getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/sequence_file"), new FileOutputStream(mdStoreV1.getHdfsPath() + "/sequence_file")); GenerateNativeStoreSparkJob .main( new String[] { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-encoding", encoding, "-dateOfCollection", dateOfCollection, "-provenance", provenance, "-xpath", xpath, "-mdStoreVersion", OBJECT_MAPPER.writeValueAsString(mdStoreV1), "-readMdStoreVersion", "", "-workflowId", "abc" }); verify(mdStoreV1); } @Test @Order(2) void testGenerateNativeStoreSparkJobIncremental() throws Exception { MDStoreVersion mdStoreV2 = prepareVersion("/eu/dnetlib/dhp/collection/mdStoreVersion_2.json"); FileUtils.forceMkdir(new File(mdStoreV2.getHdfsPath())); IOUtils .copy( getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/sequence_file"), new FileOutputStream(mdStoreV2.getHdfsPath() + "/sequence_file")); MDStoreVersion mdStoreV1 = prepareVersion("/eu/dnetlib/dhp/collection/mdStoreVersion_1.json"); GenerateNativeStoreSparkJob .main( new String[] { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-encoding", encoding, "-dateOfCollection", dateOfCollection, "-provenance", provenance, "-xpath", xpath, "-mdStoreVersion", OBJECT_MAPPER.writeValueAsString(mdStoreV2), "-readMdStoreVersion", OBJECT_MAPPER.writeValueAsString(mdStoreV1), "-workflowId", "abc" }); verify(mdStoreV2); } @Test @Order(3) void testTransformSparkJob() throws Exception { setUpVocabulary(); MDStoreVersion mdStoreV2 = prepareVersion("/eu/dnetlib/dhp/collection/mdStoreVersion_2.json"); MDStoreVersion mdStoreCleanedVersion = prepareVersion("/eu/dnetlib/dhp/collection/mdStoreCleanedVersion.json"); mockupTrasformationRule("simpleTRule", "/eu/dnetlib/dhp/transform/ext_simple.xsl"); final Map parameters = Stream.of(new String[][] { { "dateOfTransformation", "1234" }, { "transformationPlugin", "XSLT_TRANSFORM" }, { "transformationRuleId", "simpleTRule" }, }).collect(Collectors.toMap(data -> data[0], data -> data[1])); TransformSparkJobNode .transformRecords( parameters, isLookUpService, spark, mdStoreV2.getHdfsPath() + MDSTORE_DATA_PATH, mdStoreCleanedVersion.getHdfsPath(), 200); final Encoder encoder = Encoders.bean(MetadataRecord.class); final Dataset mOutput = spark .read() .format("parquet") .load(mdStoreCleanedVersion.getHdfsPath() + MDSTORE_DATA_PATH) .as(encoder); final Long total = mOutput.count(); final long recordTs = mOutput .filter((FilterFunction) p -> p.getDateOfTransformation() == 1234) .count(); final long recordNotEmpty = mOutput .filter((FilterFunction) p -> !StringUtils.isBlank(p.getBody())) .count(); assertEquals(total, recordTs); assertEquals(total, recordNotEmpty); } @Test void testJSONSerialization() throws Exception { final String s = IOUtils.toString(getClass().getResourceAsStream("mdStoreVersion_1.json")); System.out.println("s = " + s); final ObjectMapper mapper = new ObjectMapper(); MDStoreVersion mi = mapper.readValue(s, MDStoreVersion.class); assertNotNull(mi); } @Test void testGenerationMetadataRecord() throws Exception { final String xml = IOUtils.toString(this.getClass().getResourceAsStream("./record.xml")); final MetadataRecord record = GenerateNativeStoreSparkJob .parseRecord( xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar", "ns_prefix"), System.currentTimeMillis(), null, null); assertNotNull(record.getId()); assertNotNull(record.getOriginalId()); } @Test void testEquals() throws IOException { final String xml = IOUtils.toString(this.getClass().getResourceAsStream("./record.xml")); final MetadataRecord record = GenerateNativeStoreSparkJob .parseRecord( xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar", "ns_prefix"), System.currentTimeMillis(), null, null); final MetadataRecord record1 = GenerateNativeStoreSparkJob .parseRecord( xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar", "ns_prefix"), System.currentTimeMillis(), null, null); record.setBody("ciao"); record1.setBody("mondo"); assertNotNull(record); assertNotNull(record1); assertEquals(record, record1); } protected void verify(MDStoreVersion mdStoreVersion) throws IOException { Assertions.assertTrue(new File(mdStoreVersion.getHdfsPath()).exists()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); long seqFileSize = sc .sequenceFile(mdStoreVersion.getHdfsPath() + "/sequence_file", IntWritable.class, Text.class) .count(); final Dataset mdstore = spark.read().load(mdStoreVersion.getHdfsPath() + "/store").as(encoder); long mdStoreSize = mdstore.count(); long declaredSize = Long.parseLong(IOUtils.toString(new FileReader(mdStoreVersion.getHdfsPath() + "/size"))); Assertions.assertEquals(seqFileSize, declaredSize, "the size must be equal"); Assertions.assertEquals(seqFileSize, mdStoreSize, "the size must be equal"); long uniqueIds = mdstore .map((MapFunction) MetadataRecord::getId, Encoders.STRING()) .distinct() .count(); Assertions.assertEquals(seqFileSize, uniqueIds, "the size must be equal"); } public MDStoreVersion prepareVersion(String filename) throws IOException { MDStoreVersion mdstore = OBJECT_MAPPER .readValue(IOUtils.toString(getClass().getResource(filename)), MDStoreVersion.class); mdstore.setHdfsPath(String.format(mdstore.getHdfsPath(), workingDir.toString())); return mdstore; } }