selection of the new plugin
This commit is contained in:
parent
9506d80ddc
commit
db6f774394
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@ -19,6 +19,7 @@ import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.aggregation.common.ReporterCallback;
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import eu.dnetlib.dhp.aggregation.common.ReportingJob;
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import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.base.BaseCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.file.FileCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.file.FileGZipCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin;
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@ -57,7 +58,7 @@ public class CollectorWorker extends ReportingJob {
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public void collect() throws UnknownCollectorPluginException, CollectorException, IOException {
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final String outputPath = mdStoreVersion.getHdfsPath() + SEQUENCE_FILE_NAME;
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final String outputPath = this.mdStoreVersion.getHdfsPath() + SEQUENCE_FILE_NAME;
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log.info("outputPath path is {}", outputPath);
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final CollectorPlugin plugin = getCollectorPlugin();
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@ -67,36 +68,36 @@ public class CollectorWorker extends ReportingJob {
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try (SequenceFile.Writer writer = SequenceFile
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.createWriter(
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fileSystem.getConf(),
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SequenceFile.Writer.file(new Path(outputPath)),
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SequenceFile.Writer.keyClass(IntWritable.class),
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SequenceFile.Writer.valueClass(Text.class),
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this.fileSystem.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
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.keyClass(IntWritable.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 IntWritable key = new IntWritable(counter.get());
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final Text value = new Text();
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plugin
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.collect(api, report)
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.forEach(
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content -> {
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key.set(counter.getAndIncrement());
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value.set(content);
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try {
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writer.append(key, value);
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} catch (Throwable e) {
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throw new RuntimeException(e);
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}
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});
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} catch (Throwable e) {
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report.put(e.getClass().getName(), e.getMessage());
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.collect(this.api, this.report)
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.forEach(content -> {
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key.set(counter.getAndIncrement());
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value.set(content);
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try {
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writer.append(key, value);
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} catch (final Throwable e) {
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throw new RuntimeException(e);
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}
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});
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} catch (final Throwable e) {
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this.report.put(e.getClass().getName(), e.getMessage());
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throw new CollectorException(e);
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} finally {
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shutdown();
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report.ongoing(counter.longValue(), counter.longValue());
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this.report.ongoing(counter.longValue(), counter.longValue());
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}
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}
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private void scheduleReport(AtomicInteger counter) {
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private void scheduleReport(final AtomicInteger counter) {
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schedule(new ReporterCallback() {
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@Override
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public Long getCurrent() {
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return counter.longValue();
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@ -111,31 +112,33 @@ public class CollectorWorker extends ReportingJob {
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private CollectorPlugin getCollectorPlugin() throws UnknownCollectorPluginException {
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switch (CollectorPlugin.NAME.valueOf(api.getProtocol())) {
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switch (CollectorPlugin.NAME.valueOf(this.api.getProtocol())) {
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case oai:
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return new OaiCollectorPlugin(clientParams);
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return new OaiCollectorPlugin(this.clientParams);
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case rest_json2xml:
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return new RestCollectorPlugin(clientParams);
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return new RestCollectorPlugin(this.clientParams);
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case file:
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return new FileCollectorPlugin(fileSystem);
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return new FileCollectorPlugin(this.fileSystem);
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case fileGzip:
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return new FileGZipCollectorPlugin(fileSystem);
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return new FileGZipCollectorPlugin(this.fileSystem);
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case baseDump:
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return new BaseCollectorPlugin(this.fileSystem);
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case other:
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final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
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.ofNullable(api.getParams().get("other_plugin_type"))
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.ofNullable(this.api.getParams().get("other_plugin_type"))
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.map(CollectorPlugin.NAME.OTHER_NAME::valueOf)
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.orElseThrow(() -> new IllegalArgumentException("invalid other_plugin_type"));
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switch (plugin) {
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case mdstore_mongodb_dump:
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return new MongoDbDumpCollectorPlugin(fileSystem);
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return new MongoDbDumpCollectorPlugin(this.fileSystem);
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case mdstore_mongodb:
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return new MDStoreCollectorPlugin();
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default:
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throw new UnknownCollectorPluginException("plugin is not managed: " + plugin);
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}
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default:
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throw new UnknownCollectorPluginException("protocol is not managed: " + api.getProtocol());
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throw new UnknownCollectorPluginException("protocol is not managed: " + this.api.getProtocol());
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}
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}
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@ -10,7 +10,8 @@ import eu.dnetlib.dhp.common.collection.CollectorException;
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public interface CollectorPlugin {
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enum NAME {
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oai, other, rest_json2xml, file, fileGzip;
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oai, other, rest_json2xml, file, fileGzip, baseDump;
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public enum OTHER_NAME {
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mdstore_mongodb_dump, mdstore_mongodb
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@ -52,17 +52,18 @@ public class BaseAnalyzerJob {
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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(BaseAnalyzerJob.class
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.getResourceAsStream("/eu/dnetlib/dhp/collection/plugin/base/action_set_parameters.json"));
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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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.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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@ -98,106 +99,119 @@ public class BaseAnalyzerJob {
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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("\n**************************************\n* EXECUTING STEP 0: LoadRecords\n**************************************");
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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("\n**************************************\n* EXECUTING STEP 0: DONE\n**************************************");
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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("\n**************************************\n* EXECUTING STEP 1: Base Report\n**************************************");
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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("\n**************************************\n* EXECUTING STEP 1: DONE\n**************************************");
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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("\n**************************************\n* EXECUTING STEP 2: OpenDOAR Report\n**************************************");
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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("\n**************************************\n* EXECUTING STEP 2: DONE\n**************************************");
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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("\n**************************************\n* EXECUTING STEP 3: Type Vocabulary Report\n**************************************");
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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("\n**************************************\n* EXECUTING STEP 3: DONE\n**************************************");
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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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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(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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.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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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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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 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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.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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.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) { return r2; }
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if (r2 == null) { return r1; }
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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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@ -212,15 +226,17 @@ public class BaseAnalyzerJob {
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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 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(BaseAnalyzerJob.class
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.getResourceAsStream("/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-aggregation-status.sql"));
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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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@ -256,7 +272,7 @@ public class BaseAnalyzerJob {
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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 AggregatorReport report = new AggregatorReport()) {
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final AtomicLong recordsCounter = new AtomicLong(0);
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@ -264,9 +280,12 @@ public class BaseAnalyzerJob {
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final Text value = new Text();
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try (final SequenceFile.Writer writer = SequenceFile
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.createWriter(fs.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
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.keyClass(LongWritable.class), SequenceFile.Writer
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.valueClass(Text.class), SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
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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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@ -293,21 +312,21 @@ public class BaseAnalyzerJob {
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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 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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.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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.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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@ -45,9 +45,9 @@ public class BaseCollectorPlugin implements CollectorPlugin {
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public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report) throws CollectorException {
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// get path to file
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final Path filePath = Optional
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.ofNullable(api.getBaseUrl())
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.map(Path::new)
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.orElseThrow(() -> new CollectorException("missing baseUrl"));
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.ofNullable(api.getBaseUrl())
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.map(Path::new)
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.orElseThrow(() -> new CollectorException("missing baseUrl"));
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final String dbUrl = api.getParams().get("dbUrl");
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final String dbUser = api.getParams().get("dbUser");
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@ -59,7 +59,9 @@ public class BaseCollectorPlugin implements CollectorPlugin {
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log.info("dbPassword: {}", "***");
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try {
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if (!this.fs.exists(filePath)) { throw new CollectorException("path does not exist: " + filePath); }
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if (!this.fs.exists(filePath)) {
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throw new CollectorException("path does not exist: " + filePath);
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}
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} catch (final Throwable e) {
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throw new CollectorException(e);
|
||||
}
|
||||
|
|
@ -69,18 +71,20 @@ public class BaseCollectorPlugin implements CollectorPlugin {
|
|||
final Iterator<String> iterator = new BaseCollectorIterator(this.fs, filePath, report);
|
||||
final Spliterator<String> spliterator = Spliterators.spliteratorUnknownSize(iterator, Spliterator.ORDERED);
|
||||
return StreamSupport
|
||||
.stream(spliterator, false)
|
||||
.filter(doc -> filterXml(doc, acceptedOpendoarIds, report));
|
||||
.stream(spliterator, false)
|
||||
.filter(doc -> filterXml(doc, acceptedOpendoarIds, report));
|
||||
}
|
||||
|
||||
private Set<String> findAcceptedOpendoarIds(final String dbUrl, final String dbUser, final String dbPassword) throws CollectorException {
|
||||
private Set<String> findAcceptedOpendoarIds(final String dbUrl, final String dbUser, final String dbPassword)
|
||||
throws CollectorException {
|
||||
final Set<String> accepted = new HashSet<>();
|
||||
|
||||
try (final DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
|
||||
|
||||
final String sql = IOUtils
|
||||
.toString(BaseAnalyzerJob.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql"));
|
||||
.toString(
|
||||
BaseAnalyzerJob.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql"));
|
||||
|
||||
dbClient.processResults(sql, row -> {
|
||||
try {
|
||||
|
|
|
|||
Loading…
Reference in New Issue