WIP: metadata collection in INCREMENTAL mode and relative test
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package eu.dnetlib.dhp.collection;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.FileReader;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.IntWritable;
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import org.apache.hadoop.io.Text;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoder;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
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import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
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@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
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public class GenerateNativeStoreSparkJobTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static SparkSession spark;
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private static Path workingDir;
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private static Encoder<MetadataRecord> encoder;
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private static final String encoding = "XML";
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private static final String dateOfCollection = System.currentTimeMillis() + "";
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private static final String xpath = "//*[local-name()='header']/*[local-name()='identifier']";
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private static String provenance;
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private static final Logger log = LoggerFactory.getLogger(GenerateNativeStoreSparkJobTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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provenance = IOUtils.toString(GenerateNativeStoreSparkJobTest.class.getResourceAsStream("provenance.json"));
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workingDir = Files.createTempDirectory(GenerateNativeStoreSparkJobTest.class.getSimpleName());
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log.info("using work dir {}", workingDir);
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SparkConf conf = new SparkConf();
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conf.setAppName(GenerateNativeStoreSparkJobTest.class.getSimpleName());
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conf.setMaster("local[*]");
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conf.set("spark.driver.host", "localhost");
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conf.set("hive.metastore.local", "true");
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conf.set("spark.ui.enabled", "false");
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conf.set("spark.sql.warehouse.dir", workingDir.toString());
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conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
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encoder = Encoders.bean(MetadataRecord.class);
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spark = SparkSession
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.builder()
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.appName(GenerateNativeStoreSparkJobTest.class.getSimpleName())
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.config(conf)
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.getOrCreate();
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}
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@AfterAll
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public static void afterAll() throws IOException {
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FileUtils.deleteDirectory(workingDir.toFile());
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spark.stop();
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}
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@Test
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@Order(1)
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public void testGenerateNativeStoreSparkJobRefresh() throws Exception {
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MDStoreVersion mdStoreV1 = prepareVersion("mdStoreVersion_1.json");
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FileUtils.forceMkdir(new File(mdStoreV1.getHdfsPath()));
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IOUtils
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.copy(
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getClass().getResourceAsStream("sequence_file"),
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new FileOutputStream(mdStoreV1.getHdfsPath() + "/sequence_file"));
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GenerateNativeStoreSparkJob
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-encoding", encoding,
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"-dateOfCollection", dateOfCollection,
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"-provenance", provenance,
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"-xpath", xpath,
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"-mdStoreVersion", OBJECT_MAPPER.writeValueAsString(mdStoreV1),
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"-readMdStoreVersion", "",
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"-workflowId", "abc"
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});
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verify(mdStoreV1);
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}
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@Test
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@Order(2)
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public void testGenerateNativeStoreSparkJobIncremental() throws Exception {
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MDStoreVersion mdStoreV2 = prepareVersion("mdStoreVersion_2.json");
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FileUtils.forceMkdir(new File(mdStoreV2.getHdfsPath()));
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IOUtils
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.copy(
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getClass().getResourceAsStream("sequence_file"),
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new FileOutputStream(mdStoreV2.getHdfsPath() + "/sequence_file"));
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MDStoreVersion mdStoreV1 = prepareVersion("mdStoreVersion_1.json");
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GenerateNativeStoreSparkJob
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-encoding", encoding,
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"-dateOfCollection", dateOfCollection,
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"-provenance", provenance,
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"-xpath", xpath,
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"-mdStoreVersion", OBJECT_MAPPER.writeValueAsString(mdStoreV2),
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"-readMdStoreVersion", OBJECT_MAPPER.writeValueAsString(mdStoreV1),
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"-workflowId", "abc"
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});
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verify(mdStoreV2);
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}
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protected void verify(MDStoreVersion mdStoreVersion) throws IOException {
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Assertions.assertTrue(new File(mdStoreVersion.getHdfsPath()).exists());
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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long seqFileSize = sc
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.sequenceFile(mdStoreVersion.getHdfsPath() + "/sequence_file", IntWritable.class, Text.class)
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.count();
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final Dataset<MetadataRecord> mdstore = spark.read().load(mdStoreVersion.getHdfsPath() + "/store").as(encoder);
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long mdStoreSize = mdstore.count();
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long declaredSize = Long.parseLong(IOUtils.toString(new FileReader(mdStoreVersion.getHdfsPath() + "/size")));
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Assertions.assertEquals(seqFileSize, declaredSize, "the size must be equal");
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Assertions.assertEquals(seqFileSize, mdStoreSize, "the size must be equal");
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long uniqueIds = mdstore
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.map((MapFunction<MetadataRecord, String>) MetadataRecord::getId, Encoders.STRING())
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.distinct()
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.count();
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Assertions.assertEquals(seqFileSize, uniqueIds, "the size must be equal");
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}
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private MDStoreVersion prepareVersion(String filename) throws IOException {
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MDStoreVersion mdstore = OBJECT_MAPPER
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.readValue(IOUtils.toString(getClass().getResource(filename)), MDStoreVersion.class);
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mdstore.setHdfsPath(String.format(mdstore.getHdfsPath(), workingDir.toString()));
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return mdstore;
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}
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}
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@ -1,9 +0,0 @@
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{
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"id": "md-7557225f-77cc-407d-bdf4-d2fe03131464-1611935085410",
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"mdstore": "md-7557225f-77cc-407d-bdf4-d2fe03131464",
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"writing": true,
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"readCount": 0,
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"lastUpdate": null,
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"size": 0,
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"hdfsPath": "/data/dnet.dev/mdstore/md-7557225f-77cc-407d-bdf4-d2fe03131464/md-7557225f-77cc-407d-bdf4-d2fe03131464-1611935085410"
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}
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@ -0,0 +1,9 @@
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{
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"id":"md-84e86d00-5771-4ed9-b17f-177ef4b46e42-1612187678801",
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"mdstore":"md-84e86d00-5771-4ed9-b17f-177ef4b46e42",
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"writing":true,
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"readCount":0,
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"lastUpdate":null,
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"size":0,
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"hdfsPath":"%s/mdstore/md-84e86d00-5771-4ed9-b17f-177ef4b46e42/v1"
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}
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@ -0,0 +1,9 @@
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{
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"id":"md-84e86d00-5771-4ed9-b17f-177ef4b46e42-1612187459108",
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"mdstore":"md-84e86d00-5771-4ed9-b17f-177ef4b46e42",
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"writing":false,
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"readCount":1,
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"lastUpdate":1612187563099,
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"size":71,
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"hdfsPath":"%s/mdstore/md-84e86d00-5771-4ed9-b17f-177ef4b46e42/v2"
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}
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@ -0,0 +1,5 @@
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{
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"datasourceId":"74912366-d6df-49c1-a1fd-8a52fa98ce5f_UmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZXMvUmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZVR5cGU\u003d",
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"datasourceName":"PSNC Institutional Repository",
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"nsPrefix":"psnc______pl"
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}
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