[aggregator graph] save invalid records aside for further inspection
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1e42d984e1
commit
e370e940d8
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package eu.dnetlib.dhp.oa.graph.raw;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.rdd.RDD;
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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.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.HdfsSupport;
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import scala.Tuple2;
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public class VerifyRecordsApplication {
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private static final Logger log = LoggerFactory.getLogger(VerifyRecordsApplication.class);
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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VerifyRecordsApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json")));
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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 sourcePaths = parser.get("sourcePaths");
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log.info("sourcePaths: {}", sourcePaths);
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final String invalidPath = parser.get("invalidPath");
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log.info("invalidPath: {}", invalidPath);
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final String isLookupUrl = parser.get("isLookupUrl");
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log.info("isLookupUrl: {}", isLookupUrl);
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final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
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final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService);
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final SparkConf conf = new SparkConf();
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runWithSparkSession(conf, isSparkSessionManaged, spark -> {
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HdfsSupport.remove(invalidPath, spark.sparkContext().hadoopConfiguration());
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validateRecords(spark, sourcePaths, invalidPath, vocs);
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});
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}
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private static void validateRecords(SparkSession spark, String sourcePaths, String invalidPath,
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VocabularyGroup vocs) {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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final List<String> existingSourcePaths = Arrays
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.stream(sourcePaths.split(","))
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.filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration()))
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.collect(Collectors.toList());
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log.info("Verify records in files:");
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existingSourcePaths.forEach(log::info);
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for (final String sp : existingSourcePaths) {
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RDD<String> invalidRecords = sc
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.sequenceFile(sp, Text.class, Text.class)
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.map(k -> tryApplyMapping(k._1().toString(), k._2().toString(), true, vocs))
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.filter(Objects::nonNull)
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.rdd();
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spark
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.createDataset(invalidRecords, Encoders.STRING())
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.write()
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.mode(SaveMode.Append)
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.option("compression", "gzip")
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.text(invalidPath);
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}
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}
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private static String tryApplyMapping(
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final String id,
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final String xmlRecord,
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final boolean shouldHashId,
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final VocabularyGroup vocs) {
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final List<Oaf> oaf = GenerateEntitiesApplication.convertToListOaf(id, xmlRecord, shouldHashId, vocs);
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if (Optional.ofNullable(oaf).map(List::isEmpty).orElse(false)) {
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return xmlRecord;
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}
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return null;
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}
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}
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@ -0,0 +1,26 @@
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[
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{
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"paramName": "issm",
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "when true will stop SparkSession after job execution",
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"paramRequired": false
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},
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{
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"paramName": "s",
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"paramLongName": "sourcePaths",
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"paramDescription": "the HDFS source paths which contains the sequential file (comma separated)",
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"paramRequired": true
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},
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{
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"paramName": "i",
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"paramLongName": "invalidPath",
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"paramDescription": "the path of the invalid records file",
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"paramRequired": false
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},
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{
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"paramName": "isu",
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"paramLongName": "isLookupUrl",
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"paramDescription": "the url of the ISLookupService",
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"paramRequired": true
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}
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]
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