authors and works are now updated in two separate spark actions of the wf
parent
858efbfad1
commit
efe4c2a9c5
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package eu.dnetlib.doiboost.orcid;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.IOException;
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import java.util.Objects;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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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.api.java.function.Function;
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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.util.LongAccumulator;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.annotation.JsonInclude;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonParser;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.orcid.AuthorSummary;
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import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;
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import scala.Tuple2;
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public class SparkUpdateOrcidAuthors {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
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.setSerializationInclusion(JsonInclude.Include.NON_NULL);
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public static void main(String[] args) throws IOException, Exception {
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Logger logger = LoggerFactory.getLogger(SparkUpdateOrcidDatasets.class);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkUpdateOrcidDatasets.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/download_orcid_data.json")));
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parser.parseArgument(args);
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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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final String workingPath = parser.get("workingPath");
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// final String outputPath = parser.get("outputPath");
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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LongAccumulator oldAuthorsFoundAcc = spark
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.sparkContext()
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.longAccumulator("old_authors_found");
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LongAccumulator updatedAuthorsFoundAcc = spark
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.sparkContext()
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.longAccumulator("updated_authors_found");
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LongAccumulator newAuthorsFoundAcc = spark
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.sparkContext()
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.longAccumulator("new_authors_found");
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LongAccumulator errorCodeAuthorsFoundAcc = spark
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.sparkContext()
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.longAccumulator("error_code_authors_found");
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LongAccumulator errorLoadingAuthorsJsonFoundAcc = spark
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.sparkContext()
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.longAccumulator("error_loading_authors_json_found");
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LongAccumulator errorParsingAuthorsXMLFoundAcc = spark
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.sparkContext()
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.longAccumulator("error_parsing_authors_xml_found");
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Function<Tuple2<Text, Text>, AuthorSummary> retrieveAuthorSummaryFunction = data -> {
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AuthorSummary authorSummary = new AuthorSummary();
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String orcidId = data._1().toString();
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String jsonData = data._2().toString();
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JsonElement jElement = new JsonParser().parse(jsonData);
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String statusCode = getJsonValue(jElement, "statusCode");
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String downloadDate = getJsonValue(jElement, "lastModifiedDate");
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if (statusCode.equals("200")) {
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String compressedData = getJsonValue(jElement, "compressedData");
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if (StringUtils.isEmpty(compressedData)) {
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errorLoadingAuthorsJsonFoundAcc.add(1);
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} else {
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String xmlAuthor = ArgumentApplicationParser.decompressValue(compressedData);
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try {
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authorSummary = XMLRecordParser
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.VTDParseAuthorSummary(xmlAuthor.getBytes());
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authorSummary.setStatusCode(statusCode);
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authorSummary.setDownloadDate("2020-11-18 00:00:05.644768");
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authorSummary.setBase64CompressData(compressedData);
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return authorSummary;
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} catch (Exception e) {
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logger.error("parsing xml " + orcidId + " [" + jsonData + "]", e);
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errorParsingAuthorsXMLFoundAcc.add(1);
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}
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}
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} else {
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authorSummary.setStatusCode(statusCode);
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authorSummary.setDownloadDate("2020-11-18 00:00:05.644768");
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errorCodeAuthorsFoundAcc.add(1);
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}
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return authorSummary;
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};
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Dataset<AuthorSummary> downloadedAuthorSummaryDS = spark
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.createDataset(
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sc
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.sequenceFile(workingPath + "downloads/updated_authors/*", Text.class, Text.class)
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.map(retrieveAuthorSummaryFunction)
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.rdd(),
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Encoders.bean(AuthorSummary.class));
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Dataset<AuthorSummary> currentAuthorSummaryDS = spark
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.createDataset(
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sc
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.textFile(workingPath.concat("orcid_dataset/authors/*"))
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.map(item -> OBJECT_MAPPER.readValue(item, AuthorSummary.class))
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.rdd(),
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Encoders.bean(AuthorSummary.class));
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currentAuthorSummaryDS
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.joinWith(
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downloadedAuthorSummaryDS,
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currentAuthorSummaryDS
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.col("authorData.oid")
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.equalTo(downloadedAuthorSummaryDS.col("authorData.oid")),
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"full_outer")
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.map(value -> {
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Optional<AuthorSummary> opCurrent = Optional.ofNullable(value._1());
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Optional<AuthorSummary> opDownloaded = Optional.ofNullable(value._2());
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if (!opCurrent.isPresent()) {
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newAuthorsFoundAcc.add(1);
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return opDownloaded.get();
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}
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if (!opDownloaded.isPresent()) {
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oldAuthorsFoundAcc.add(1);
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return opCurrent.get();
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}
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if (opCurrent.isPresent() && opDownloaded.isPresent()) {
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updatedAuthorsFoundAcc.add(1);
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return opDownloaded.get();
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}
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return null;
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},
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Encoders.bean(AuthorSummary.class))
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.filter(Objects::nonNull)
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.toJavaRDD()
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.map(authorSummary -> OBJECT_MAPPER.writeValueAsString(authorSummary))
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.saveAsTextFile(workingPath.concat("orcid_dataset/new_authors"), GzipCodec.class);
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logger.info("oldAuthorsFoundAcc: " + oldAuthorsFoundAcc.value().toString());
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logger.info("newAuthorsFoundAcc: " + newAuthorsFoundAcc.value().toString());
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logger.info("updatedAuthorsFoundAcc: " + updatedAuthorsFoundAcc.value().toString());
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logger.info("errorCodeFoundAcc: " + errorCodeAuthorsFoundAcc.value().toString());
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logger.info("errorLoadingJsonFoundAcc: " + errorLoadingAuthorsJsonFoundAcc.value().toString());
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logger.info("errorParsingXMLFoundAcc: " + errorParsingAuthorsXMLFoundAcc.value().toString());
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});
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}
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private static String getJsonValue(JsonElement jElement, String property) {
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if (jElement.getAsJsonObject().has(property)) {
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JsonElement name = null;
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name = jElement.getAsJsonObject().get(property);
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if (name != null && !name.isJsonNull()) {
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return name.getAsString();
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}
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}
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return "";
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}
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}
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@ -0,0 +1,181 @@
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package eu.dnetlib.doiboost.orcid;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.IOException;
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import java.util.Objects;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.hadoop.io.compress.GzipCodec;
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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.api.java.function.Function;
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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.util.LongAccumulator;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.annotation.JsonInclude;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonParser;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.orcid.Work;
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import eu.dnetlib.dhp.schema.orcid.WorkDetail;
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import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi;
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public class SparkUpdateOrcidWorks {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
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.setSerializationInclusion(JsonInclude.Include.NON_NULL);
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public static void main(String[] args) throws IOException, Exception {
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Logger logger = LoggerFactory.getLogger(SparkUpdateOrcidDatasets.class);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkUpdateOrcidDatasets.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/download_orcid_data.json")));
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parser.parseArgument(args);
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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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final String workingPath = parser.get("workingPath");
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// final String outputPath = parser.get("outputPath");
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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LongAccumulator oldWorksFoundAcc = spark
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.sparkContext()
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.longAccumulator("old_works_found");
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LongAccumulator updatedWorksFoundAcc = spark
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.sparkContext()
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.longAccumulator("updated_works_found");
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LongAccumulator newWorksFoundAcc = spark
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.sparkContext()
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.longAccumulator("new_works_found");
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LongAccumulator errorCodeWorksFoundAcc = spark
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.sparkContext()
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.longAccumulator("error_code_works_found");
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LongAccumulator errorLoadingWorksJsonFoundAcc = spark
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.sparkContext()
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.longAccumulator("error_loading_works_json_found");
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LongAccumulator errorParsingWorksXMLFoundAcc = spark
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.sparkContext()
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.longAccumulator("error_parsing_works_xml_found");
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Function<String, Work> retrieveWorkFunction = jsonData -> {
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Work work = new Work();
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JsonElement jElement = new JsonParser().parse(jsonData);
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String statusCode = getJsonValue(jElement, "statusCode");
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work.setStatusCode(statusCode);
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String downloadDate = getJsonValue(jElement, "lastModifiedDate");
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work.setDownloadDate("2020-11-18 00:00:05.644768");
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if (statusCode.equals("200")) {
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String compressedData = getJsonValue(jElement, "compressedData");
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if (StringUtils.isEmpty(compressedData)) {
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errorLoadingWorksJsonFoundAcc.add(1);
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} else {
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String xmlWork = ArgumentApplicationParser.decompressValue(compressedData);
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try {
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WorkDetail workDetail = XMLRecordParserNoDoi
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.VTDParseWorkData(xmlWork.getBytes());
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work.setWorkDetail(workDetail);
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work.setBase64CompressData(compressedData);
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return work;
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} catch (Exception e) {
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logger.error("parsing xml [" + jsonData + "]", e);
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errorParsingWorksXMLFoundAcc.add(1);
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}
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}
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} else {
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errorCodeWorksFoundAcc.add(1);
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}
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return work;
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};
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Dataset<Work> downloadedWorksDS = spark
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.createDataset(
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sc
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.textFile(workingPath + "downloads/updated_works/*")
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.map(s -> {
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return s.substring(21, s.length() - 1);
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})
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.map(retrieveWorkFunction)
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.rdd(),
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Encoders.bean(Work.class));
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Dataset<Work> currentWorksDS = spark
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.createDataset(
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sc
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.textFile(workingPath.concat("orcid_dataset/works/*"))
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.map(item -> OBJECT_MAPPER.readValue(item, Work.class))
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.rdd(),
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Encoders.bean(Work.class));
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currentWorksDS
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.joinWith(
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downloadedWorksDS,
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currentWorksDS
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.col("workDetail.id")
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.equalTo(downloadedWorksDS.col("workDetail.id"))
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.and(
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currentWorksDS
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.col("workDetail.oid")
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.equalTo(downloadedWorksDS.col("workDetail.oid"))),
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"full_outer")
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.map(value -> {
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Optional<Work> opCurrent = Optional.ofNullable(value._1());
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Optional<Work> opDownloaded = Optional.ofNullable(value._2());
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if (!opCurrent.isPresent()) {
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newWorksFoundAcc.add(1);
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return opDownloaded.get();
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}
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if (!opDownloaded.isPresent()) {
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oldWorksFoundAcc.add(1);
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return opCurrent.get();
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}
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if (opCurrent.isPresent() && opDownloaded.isPresent()) {
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updatedWorksFoundAcc.add(1);
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return opDownloaded.get();
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}
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return null;
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},
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Encoders.bean(Work.class))
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.filter(Objects::nonNull)
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.toJavaRDD()
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.map(work -> OBJECT_MAPPER.writeValueAsString(work))
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.saveAsTextFile(workingPath.concat("orcid_dataset/new_works"), GzipCodec.class);
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logger.info("oldWorksFoundAcc: " + oldWorksFoundAcc.value().toString());
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logger.info("newWorksFoundAcc: " + newWorksFoundAcc.value().toString());
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logger.info("updatedWorksFoundAcc: " + updatedWorksFoundAcc.value().toString());
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logger.info("errorCodeWorksFoundAcc: " + errorCodeWorksFoundAcc.value().toString());
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logger.info("errorLoadingJsonWorksFoundAcc: " + errorLoadingWorksJsonFoundAcc.value().toString());
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logger.info("errorParsingXMLWorksFoundAcc: " + errorParsingWorksXMLFoundAcc.value().toString());
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});
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}
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private static String getJsonValue(JsonElement jElement, String property) {
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if (jElement.getAsJsonObject().has(property)) {
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JsonElement name = null;
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name = jElement.getAsJsonObject().get(property);
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if (name != null && !name.isJsonNull()) {
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return name.getAsString();
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}
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}
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return "";
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}
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}
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