OpenDoar reports
This commit is contained in:
parent
f8cf7ffbcb
commit
3d14bef381
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@ -2,8 +2,10 @@
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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.io.IOException;
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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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@ -12,7 +14,9 @@ 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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@ -23,6 +27,7 @@ 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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@ -35,6 +40,7 @@ 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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public class BaseAnalyzerJob {
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@ -68,78 +74,181 @@ public class BaseAnalyzerJob {
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}: ", outputPath);
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final boolean reimport = Boolean.parseBoolean(parser.get("reimport"));
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log.info("reimport {}: ", reimport);
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final String opendoarPath = parser.get("opendoarPath");
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log.info("opendoarPath {}: ", opendoarPath);
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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(
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conf, isSparkSessionManaged, spark -> processBaseRecords(spark, inputPath, dataPath, outputPath, reimport));
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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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});
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}
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private static void processBaseRecords(final SparkSession spark,
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final String inputPath,
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final String dataPath,
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final String outputPath,
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final boolean reimport) throws IOException {
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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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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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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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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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repo.getAggregations().put(api, count);
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}
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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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if (reimport) {
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loadRecords(fs, inputPath, dataPath, report);
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}
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final AtomicLong recordsCounter = new AtomicLong(0);
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// fs.delete(new Path(outputPath), true);
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extractInfo(spark, dataPath, outputPath);
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} catch (final Throwable e) {
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throw new RuntimeException(e);
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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 loadRecords(final FileSystem fs,
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final String inputPath,
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final String outputPath,
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final AggregatorReport report)
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throws Exception {
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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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private static void extractInfo(final SparkSession spark,
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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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@ -33,7 +33,7 @@ public class BaseCollectorIterator implements Iterator<String> {
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private String nextElement;
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private final BlockingQueue<String> queue = new LinkedBlockingQueue<>(20);
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private final BlockingQueue<String> queue = new LinkedBlockingQueue<>(100);
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private static final Logger log = LoggerFactory.getLogger(BaseCollectorIterator.class);
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@ -0,0 +1,42 @@
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package eu.dnetlib.dhp.collection.plugin.base;
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import java.io.Serializable;
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import java.util.HashMap;
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import java.util.Map;
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public class OpenDoarRepoStatus implements Serializable {
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private static final long serialVersionUID = 4832658700366871160L;
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private String id;
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private String jurisdiction;
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private Map<String, Long> aggregations = new HashMap<>();
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public String getId() {
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return this.id;
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}
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public void setId(final String id) {
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this.id = id;
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}
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public String getJurisdiction() {
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return this.jurisdiction;
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}
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public void setJurisdiction(final String jurisdiction) {
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this.jurisdiction = jurisdiction;
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}
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public Map<String, Long> getAggregations() {
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return this.aggregations;
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}
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public void setAggregations(final Map<String, Long> aggregations) {
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this.aggregations = aggregations;
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}
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}
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@ -14,13 +14,37 @@
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{
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"paramName": "o",
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"paramLongName": "outputPath",
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"paramDescription": "the path of the generated report",
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"paramDescription": "the path of the generated the report",
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"paramRequired": true
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},
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{
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"paramName": "r",
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"paramLongName": "reimport",
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"paramDescription": "complete re-import",
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"paramName": "od",
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"paramLongName": "opendoarPath",
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"paramDescription": "the path of the generated the OpenDOAR report",
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"paramRequired": true
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},
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{
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"paramName": "f",
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"paramLongName": "fromStep",
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"paramDescription": "the initial step (numeric, 0 for ALL STEPS)",
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"paramRequired": true
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},
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{
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"paramName": "pgurl",
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"paramLongName": "postgresUrl",
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"paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb",
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"paramRequired": true
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},
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{
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"paramName": "pguser",
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"paramLongName": "postgresUser",
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"paramDescription": "postgres user",
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"paramRequired": false
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},
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{
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"paramName": "pgpasswd",
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"paramLongName": "postgresPassword",
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"paramDescription": "postgres password",
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"paramRequired": false
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}
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]
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@ -13,8 +13,24 @@
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<description>path where to store the reports</description>
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</property>
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<property>
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<name>baseReimportFlag</name>
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<description>flag to re-import the records from dump</description>
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<name>baseOpenDoarReportsPath</name>
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<description>path where to store the OpenDOAR reports</description>
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</property>
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<property>
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<name>postgresURL</name>
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<description>the postgres URL to access to the database</description>
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</property>
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<property>
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<name>postgresUser</name>
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<description>the user postgres</description>
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</property>
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<property>
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<name>postgresPassword</name>
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<description>the password postgres</description>
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</property>
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<property>
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<name>baseFromStep</name>
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<description>the initial step (numeric, 0 for ALL STEPS)</description>
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</property>
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</parameters>
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@ -44,7 +60,11 @@
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<arg>--inputPath</arg><arg>${baseInputPath}</arg>
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<arg>--dataPath</arg><arg>${baseDataPath}</arg>
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<arg>--outputPath</arg><arg>${baseReportsPath}</arg>
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<arg>--reimport</arg><arg>${baseReimportFlag}</arg>
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<arg>--opendoarPath</arg><arg>${baseOpenDoarReportsPath}</arg>
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<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
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<arg>--postgresUser</arg><arg>${postgresUser}</arg>
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<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
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<arg>--fromStep</arg><arg>${baseFromStep}</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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@ -0,0 +1,11 @@
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select
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s.id as id,
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s.jurisdiction as jurisdiction,
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array_remove(array_agg(a.id || ' (' || coalesce(a.compatibility_override, a.compatibility, 'UNKNOWN') || '):' || coalesce(a.last_collection_total, 0)), NULL) as aggregations
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from
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dsm_services s
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join dsm_api a on (s.id = a.service)
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where
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collectedfrom = 'openaire____::opendoar'
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group by
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s.id;
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