dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkUpdateOrcidDatasets.java

318 lines
12 KiB
Java

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