first implementation of Hdfs Mdstores Importer

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java

@@ -0,0 +1,120 @@
+
+package eu.dnetlib.dhp.oa.graph.raw;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.util.Arrays;
+import java.util.Optional;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
+import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo;
+
+public class MigrateHdfsMdstoresApplication extends AbstractMigrationApplication {
+
+	private static final Logger log = LoggerFactory.getLogger(MigrateHdfsMdstoresApplication.class);
+
+	private final String mdstoreManagerUrl;
+
+	private final String format;
+
+	private final String layout;
+
+	private final String interpretation;
+
+	public static void main(final String[] args) throws Exception {
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(MigrateHdfsMdstoresApplication.class
+					.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_hdfs_mstores_parameters.json")));
+		parser.parseArgument(args);
+
+		final Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String mdstoreManagerUrl = parser.get("mdstoreManagerUrl");
+		final String mdFormat = parser.get("mdFormat");
+		final String mdLayout = parser.get("mdLayout");
+		final String mdInterpretation = parser.get("mdInterpretation");
+
+		final String hdfsPath = parser.get("hdfsPath");
+
+		final SparkConf conf = new SparkConf();
+		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
+			try (final MigrateHdfsMdstoresApplication app =
+				new MigrateHdfsMdstoresApplication(hdfsPath, mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation)) {
+				app.execute(spark);
+			}
+		});
+	}
+
+	public MigrateHdfsMdstoresApplication(final String hdfsPath, final String mdstoreManagerUrl, final String format, final String layout,
+		final String interpretation) throws Exception {
+		super(hdfsPath);
+		this.mdstoreManagerUrl = mdstoreManagerUrl;
+		this.format = format;
+		this.layout = layout;
+		this.interpretation = interpretation;
+	}
+
+	public void execute(final SparkSession spark) throws Exception {
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		final Set<String> paths = mdstorePaths(sc);
+		log.info("Found " + paths.size() + " not empty mdstores");
+
+		spark.read()
+			.parquet(paths.toArray(new String[paths.size()]))
+			.map((MapFunction<Row, String>) r -> r.getAs("body"), Encoders.STRING())
+			.foreach(xml -> emit(xml, String.format("%s-%s-%s", format, layout, interpretation)));
+	}
+
+	private Set<String> mdstorePaths(final JavaSparkContext sc) throws Exception {
+		final String url = mdstoreManagerUrl + "/mdstores";
+		final ObjectMapper objectMapper = new ObjectMapper();
+
+		final HttpGet req = new HttpGet(url);
+
+		try (final CloseableHttpClient client = HttpClients.createDefault()) {
+			try (final CloseableHttpResponse response = client.execute(req)) {
+				final String json = IOUtils.toString(response.getEntity().getContent());
+				final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class);
+				return Arrays.stream(mdstores)
+					.filter(md -> md.getFormat().equalsIgnoreCase(format))
+					.filter(md -> md.getLayout().equalsIgnoreCase(layout))
+					.filter(md -> md.getInterpretation().equalsIgnoreCase(interpretation))
+					.filter(md -> StringUtils.isNotBlank(md.getHdfsPath()))
+					.filter(md -> StringUtils.isNotBlank(md.getCurrentVersion()))
+					.filter(md -> md.getSize() > 0)
+					.map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store")
+					.filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration()))
+					.collect(Collectors.toSet());
+			}
+		}
+	}
+
+}

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_hdfs_mstores_parameters.json

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+[
+	{
+		"paramName": "p",
+		"paramLongName": "hdfsPath",
+		"paramDescription": "the path where storing the sequential file",
+		"paramRequired": true
+	},
+	{
+		"paramName": "u",
+		"paramLongName": "mdstoreManagerUrl",
+		"paramDescription": "the MdstoreManager url",
+		"paramRequired": true
+	},
+	{
+		"paramName": "f",
+		"paramLongName": "mdFormat",
+		"paramDescription": "metadata format",
+		"paramRequired": true
+	},
+	{
+		"paramName": "l",
+		"paramLongName": "mdLayout",
+		"paramDescription": "metadata layout",
+		"paramRequired": true
+	},
+	{
+		"paramName": "i",
+		"paramLongName": "mdInterpretation",
+		"paramDescription": "metadata interpretation",
+		"paramRequired": true
+	}
+]