380 lines
12 KiB
Java
380 lines
12 KiB
Java
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package eu.dnetlib.dhp.collection.plugin.base;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import static org.apache.spark.sql.functions.col;
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import static org.apache.spark.sql.functions.count;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.LinkedHashSet;
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import java.util.List;
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import java.util.Optional;
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import java.util.Set;
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import java.util.concurrent.atomic.AtomicLong;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.ObjectUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.math.NumberUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.hadoop.io.LongWritable;
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import org.apache.hadoop.io.SequenceFile;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.DeflateCodec;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.DocumentHelper;
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import org.dom4j.Element;
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import org.dom4j.Node;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.DbClient;
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import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
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import scala.Tuple2;
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public class BaseAnalyzerJob {
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private static final String BASE_DUMP = "BASE_DUMP";
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private static final Logger log = LoggerFactory.getLogger(BaseAnalyzerJob.class);
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public static void main(final String[] args) throws Exception {
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final String jsonConfiguration = IOUtils
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.toString(
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BaseAnalyzerJob.class
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.getResourceAsStream("/eu/dnetlib/dhp/collection/plugin/base/action_set_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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final Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("inputPath");
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log.info("inputPath: {}", inputPath);
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final String dataPath = parser.get("dataPath");
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log.info("dataPath {}: ", dataPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}: ", outputPath);
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final String opendoarPath = parser.get("opendoarPath");
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log.info("opendoarPath {}: ", opendoarPath);
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final String typesReportPath = parser.get("typesReportPath");
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log.info("typesReportPath {}: ", typesReportPath);
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final int fromStep = Integer.parseInt(parser.get("fromStep"));
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log.info("fromStep {}: ", fromStep);
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final String dbUrl = parser.get("postgresUrl");
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log.info("postgresUrl {}: ", dbUrl);
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final String dbUser = parser.get("postgresUser");
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log.info("postgresUser {}: ", dbUser);
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final String dbPassword = parser.get("postgresPassword");
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log.info("postgresPassword {}: ", dbPassword);
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final SparkConf conf = new SparkConf();
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runWithSparkSession(conf, isSparkSessionManaged, spark -> {
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if (fromStep <= 0) {
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log
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.info(
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"\n**************************************\n* EXECUTING STEP 0: LoadRecords\n**************************************");
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loadRecords(inputPath, dataPath);
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log
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.info(
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"\n**************************************\n* EXECUTING STEP 0: DONE\n**************************************");
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}
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if (fromStep <= 1) {
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log
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.info(
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"\n**************************************\n* EXECUTING STEP 1: Base Report\n**************************************");
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generateReport(spark, dataPath, outputPath);
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log
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.info(
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"\n**************************************\n* EXECUTING STEP 1: DONE\n**************************************");
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}
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if (fromStep <= 2) {
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log
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.info(
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"\n**************************************\n* EXECUTING STEP 2: OpenDOAR Report\n**************************************");
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generateOpenDoarReport(spark, outputPath, opendoarPath, loadOpenDoarStats(dbUrl, dbUser, dbPassword));
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log
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.info(
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"\n**************************************\n* EXECUTING STEP 2: DONE\n**************************************");
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}
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if (fromStep <= 3) {
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log
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.info(
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"\n**************************************\n* EXECUTING STEP 3: Type Vocabulary Report\n**************************************");
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generateVocTypeReport(spark, outputPath, typesReportPath);
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log
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.info(
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"\n**************************************\n* EXECUTING STEP 3: DONE\n**************************************");
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}
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});
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}
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private static void generateVocTypeReport(final SparkSession spark,
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final String reportPath,
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final String typesReportPath) {
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spark
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.read()
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.parquet(reportPath)
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.as(Encoders.bean(BaseRecordInfo.class))
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.flatMap(rec -> {
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final List<Tuple2<String, String>> list = new ArrayList<>();
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for (final String t1 : rec.getTypes()) {
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if (t1.startsWith("TYPE_NORM:")) {
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for (final String t2 : rec.getTypes()) {
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if (t2.startsWith("TYPE:")) {
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list
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.add(
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new Tuple2<>(StringUtils.substringAfter(t1, "TYPE_NORM:").trim(),
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StringUtils.substringAfter(t2, "TYPE:").trim()));
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}
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}
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}
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}
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return list.iterator();
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}, Encoders.tuple(Encoders.STRING(), Encoders.STRING()))
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.distinct()
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.write()
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.mode(SaveMode.Overwrite)
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.format("parquet")
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.save(typesReportPath);
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}
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private static void generateOpenDoarReport(final SparkSession spark,
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final String reportPath,
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final String opendoarPath,
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final List<OpenDoarRepoStatus> repos) {
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final Dataset<OpenDoarRepoStatus> fromDB = spark.createDataset(repos, Encoders.bean(OpenDoarRepoStatus.class));
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final Dataset<OpenDoarRepoStatus> fromBASE = spark
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.read()
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.parquet(reportPath)
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.selectExpr("explode(collections) as collection")
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.where("isnotnull(collection.opendoarId) and character_length(collection.opendoarId)>0")
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.selectExpr("concat('opendoar____::',collection.opendoarId) as id")
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.groupBy(col("id"))
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.agg(count(col("id")))
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.map(row -> {
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final OpenDoarRepoStatus repo = new OpenDoarRepoStatus();
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repo.setId(row.getString(0));
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repo.getAggregations().put(BASE_DUMP, row.getLong(1));
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repo.setBaseCount(row.getLong(1));
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repo.setOpenaireCount(0);
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repo.setHighCompliance(false);
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return repo;
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}, Encoders.bean(OpenDoarRepoStatus.class));
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fromDB
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.joinWith(fromBASE, fromDB.col("id").equalTo(fromBASE.col("id")), "full_outer")
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.map(t -> merge(t._1, t._2), Encoders.bean(OpenDoarRepoStatus.class))
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.write()
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.mode(SaveMode.Overwrite)
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.format("parquet")
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.save(opendoarPath);
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}
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private static OpenDoarRepoStatus merge(final OpenDoarRepoStatus r1, final OpenDoarRepoStatus r2) {
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if (r1 == null) {
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return r2;
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}
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if (r2 == null) {
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return r1;
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}
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final OpenDoarRepoStatus r = new OpenDoarRepoStatus();
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r.setId(ObjectUtils.firstNonNull(r1.getId(), r2.getId()));
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r.setJurisdiction(ObjectUtils.firstNonNull(r1.getJurisdiction(), r2.getJurisdiction()));
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r.getAggregations().putAll(r1.getAggregations());
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r.getAggregations().putAll(r2.getAggregations());
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r.setHighCompliance(r1.isHighCompliance() || r2.isHighCompliance());
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r.setBaseCount(Math.max(r1.getBaseCount(), r2.getBaseCount()));
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r.setOpenaireCount(Math.max(r1.getOpenaireCount(), r2.getOpenaireCount()));
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return r;
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}
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private static List<OpenDoarRepoStatus> loadOpenDoarStats(final String dbUrl,
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final String dbUser,
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final String dbPassword) throws Exception {
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final List<OpenDoarRepoStatus> repos = new ArrayList<>();
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try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
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final String sql = IOUtils
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.toString(
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BaseAnalyzerJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-aggregation-status.sql"));
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dbClient.processResults(sql, row -> {
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try {
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final OpenDoarRepoStatus repo = new OpenDoarRepoStatus();
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repo.setId(row.getString("id"));
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repo.setJurisdiction(row.getString("jurisdiction"));
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repo.setBaseCount(0);
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repo.setHighCompliance(false);
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long sum = 0;
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for (final String s : (String[]) row.getArray("aggregations").getArray()) {
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final String api = StringUtils.substringBefore(s, "@@@");
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final long count = NumberUtils.toLong(StringUtils.substringAfter(s, "@@@"), 0);
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sum += count;
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repo.getAggregations().put(api, count);
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// This should recognize the HIGH Compliances: openaire*X.Y*
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if (s.contains("compliance: openaire")) {
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repo.setHighCompliance(true);
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}
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}
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repo.setOpenaireCount(sum);
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repos.add(repo);
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log.info("# FOUND OPENDOAR (DB): " + repo.getId());
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} catch (final SQLException e) {
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log.error("Error in SQL", e);
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throw new RuntimeException("Error in SQL", e);
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}
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});
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}
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return repos;
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}
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private static void loadRecords(final String inputPath, final String outputPath) throws Exception {
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try (final FileSystem fs = FileSystem.get(new Configuration());
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final AggregatorReport report = new AggregatorReport()) {
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final AtomicLong recordsCounter = new AtomicLong(0);
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final LongWritable key = new LongWritable();
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final Text value = new Text();
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try (final SequenceFile.Writer writer = SequenceFile
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.createWriter(
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fs.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
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.keyClass(LongWritable.class),
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SequenceFile.Writer
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.valueClass(Text.class),
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SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
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final BaseCollectorIterator iteraror = new BaseCollectorIterator(fs, new Path(inputPath), report);
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while (iteraror.hasNext()) {
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final String record = iteraror.next();
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final long i = recordsCounter.incrementAndGet();
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if ((i % 10000) == 0) {
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log.info("# Loaded records: " + i);
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}
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key.set(i);
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value.set(record);
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try {
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writer.append(key, value);
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} catch (final Throwable e1) {
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throw new RuntimeException(e1);
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}
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}
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log.info("# COMPLETED - Loaded records: " + recordsCounter.get());
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}
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}
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}
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private static void generateReport(final SparkSession spark,
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final String inputPath,
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final String targetPath) throws Exception {
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final JavaRDD<BaseRecordInfo> rdd = JavaSparkContext
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.fromSparkContext(spark.sparkContext())
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.sequenceFile(inputPath, LongWritable.class, Text.class)
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.map(s -> s._2.toString())
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.map(BaseAnalyzerJob::extractInfo);
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spark
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.createDataset(rdd.rdd(), Encoders.bean(BaseRecordInfo.class))
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.write()
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.mode(SaveMode.Overwrite)
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.format("parquet")
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.save(targetPath);
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}
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protected static BaseRecordInfo extractInfo(final String s) {
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try {
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final Document record = DocumentHelper.parseText(s);
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final BaseRecordInfo info = new BaseRecordInfo();
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final Set<String> paths = new LinkedHashSet<>();
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final Set<String> types = new LinkedHashSet<>();
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final List<BaseCollectionInfo> colls = new ArrayList<>();
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for (final Object o : record.selectNodes("//*|//@*")) {
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paths.add(((Node) o).getPath());
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if (o instanceof Element) {
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final Element n = (Element) o;
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final String nodeName = n.getName();
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if ("collection".equals(nodeName)) {
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final String collName = n.getText().trim();
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if (StringUtils.isNotBlank(collName)) {
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final BaseCollectionInfo coll = new BaseCollectionInfo();
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coll.setId(collName);
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coll.setOpendoarId(n.valueOf("@opendoar_id").trim());
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coll.setRorId(n.valueOf("@ror_id").trim());
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colls.add(coll);
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}
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} else if ("type".equals(nodeName)) {
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types.add("TYPE: " + n.getText().trim());
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} else if ("typenorm".equals(nodeName)) {
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types.add("TYPE_NORM: " + n.getText().trim());
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}
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}
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}
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info.setId(record.valueOf("//*[local-name() = 'header']/*[local-name() = 'identifier']").trim());
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info.getTypes().addAll(types);
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info.getPaths().addAll(paths);
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info.setCollections(colls);
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return info;
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} catch (final DocumentException e) {
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throw new RuntimeException(e);
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}
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}
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}
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