forked from D-Net/dnet-hadoop
fix dataset creation for downloaded works
This commit is contained in:
parent
2233750a37
commit
858efbfad1
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@ -3,6 +3,8 @@ package eu.dnetlib.dhp.schema.orcid;
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public class OrcidData {
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protected String base64CompressData;
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protected String statusCode;
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protected String downloadDate;
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public String getBase64CompressData() {
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return base64CompressData;
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@ -11,4 +13,20 @@ public class OrcidData {
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public void setBase64CompressData(String base64CompressData) {
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this.base64CompressData = base64CompressData;
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}
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public String getStatusCode() {
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return statusCode;
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}
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public void setStatusCode(String statusCode) {
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this.statusCode = statusCode;
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}
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public String getDownloadDate() {
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return downloadDate;
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}
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public void setDownloadDate(String downloadDate) {
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this.downloadDate = downloadDate;
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}
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}
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@ -4,30 +4,47 @@ 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.Optional;
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import java.util.*;
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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.JavaPairRDD;
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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.api.java.function.FlatMapFunction;
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import org.apache.spark.api.java.function.Function;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.PairFunction;
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import org.apache.spark.rdd.RDD;
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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.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.dhp.schema.orcid.Work;
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import eu.dnetlib.dhp.schema.orcid.WorkDetail;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;
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import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter;
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import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi;
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import scala.Tuple2;
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public class SparkUpdateOrcidDatasets {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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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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logger.info("[ SparkUpdateOrcidDatasets STARTED]");
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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@ -40,11 +57,8 @@ public class SparkUpdateOrcidDatasets {
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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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logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String workingPath = parser.get("workingPath");
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logger.info("workingPath: ", workingPath);
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// final String outputPath = parser.get("outputPath");
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// logger.info("outputPath: ", outputPath);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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@ -53,35 +67,247 @@ public class SparkUpdateOrcidDatasets {
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spark -> {
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaPairRDD<Text, Text> xmlSummariesRDD = sc
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.sequenceFile(workingPath.concat("xml/authors/xml_authors.seq"), Text.class, Text.class);
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xmlSummariesRDD
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.map(seq -> {
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AuthorSummary authorSummary = XMLRecordParser
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.VTDParseAuthorSummary(seq._2().toString().getBytes());
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authorSummary
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.setBase64CompressData(ArgumentApplicationParser.compressArgument(seq._2().toString()));
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return authorSummary;
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})
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.filter(authorSummary -> authorSummary != null)
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.map(authorSummary -> JsonWriter.create(authorSummary))
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.saveAsTextFile(workingPath.concat("orcid_dataset/authors"), GzipCodec.class);
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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 errorLoadingAuthorsXMLFoundAcc = spark
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.sparkContext()
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.longAccumulator("error_loading_authors_xml_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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JavaPairRDD<Text, Text> xmlWorksRDD = sc
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.sequenceFile(workingPath.concat("xml/works/*"), Text.class, Text.class);
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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 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 errorLoadingWorksXMLFoundAcc = spark
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.sparkContext()
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.longAccumulator("error_loading_works_xml_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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xmlWorksRDD
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.map(seq -> {
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WorkDetail workDetail = XMLRecordParserNoDoi.VTDParseWorkData(seq._2().toString().getBytes());
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Work work = new Work();
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work.setWorkDetail(workDetail);
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work.setBase64CompressData(ArgumentApplicationParser.compressArgument(seq._2().toString()));
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return work;
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})
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.filter(work -> work != null)
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// JavaPairRDD<Text, Text> xmlSummariesRDD = sc
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// .sequenceFile(workingPath.concat("xml/authors/xml_authors.seq"), Text.class, Text.class);
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// xmlSummariesRDD
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// .map(seq -> {
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// AuthorSummary authorSummary = XMLRecordParser
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// .VTDParseAuthorSummary(seq._2().toString().getBytes());
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// authorSummary
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// .setBase64CompressData(ArgumentApplicationParser.compressArgument(seq._2().toString()));
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// return authorSummary;
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// })
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// .filter(authorSummary -> authorSummary != null)
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// .map(authorSummary -> JsonWriter.create(authorSummary))
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// .saveAsTextFile(workingPath.concat("orcid_dataset/authors"), GzipCodec.class);
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//
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// JavaPairRDD<Text, Text> xmlWorksRDD = sc
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// .sequenceFile(workingPath.concat("xml/works/*"), Text.class, Text.class);
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//
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// xmlWorksRDD
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// .map(seq -> {
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// WorkDetail workDetail = XMLRecordParserNoDoi.VTDParseWorkData(seq._2().toString().getBytes());
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// Work work = new Work();
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// work.setWorkDetail(workDetail);
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// work.setBase64CompressData(ArgumentApplicationParser.compressArgument(seq._2().toString()));
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// return work;
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// })
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// .filter(work -> work != null)
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// .map(work -> JsonWriter.create(work))
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// .saveAsTextFile(workingPath.concat("orcid_dataset/works"), GzipCodec.class);
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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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// if (StringUtils.isEmpty(xmlAuthor)) {
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// errorLoadingAuthorsXMLFoundAcc.add(1);
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// } else {
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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(downloadDate);
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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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// }
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// } else {
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// authorSummary.setStatusCode(statusCode);
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// authorSummary.setDownloadDate(downloadDate);
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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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//
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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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// return opDownloaded.get();
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// }
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// if (!opDownloaded.isPresent()) {
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// return opCurrent.get();
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// }
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// if (opCurrent.isPresent() && opDownloaded.isPresent()) {
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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 -> JsonWriter.create(authorSummary))
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// .saveAsTextFile(workingPath.concat("orcid_dataset/new_authors"), GzipCodec.class);
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//
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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("errorLoadingXMLFoundAcc: " + errorLoadingAuthorsXMLFoundAcc.value().toString());
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// logger.info("errorParsingXMLFoundAcc: " + errorParsingAuthorsXMLFoundAcc.value().toString());
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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(downloadDate);
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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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if (StringUtils.isEmpty(xmlWork)) {
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errorLoadingWorksXMLFoundAcc.add(1);
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} else {
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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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updatedWorksFoundAcc.add(1);
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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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}
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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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return opDownloaded.get();
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}
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if (!opDownloaded.isPresent()) {
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return opCurrent.get();
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}
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if (opCurrent.isPresent() && opDownloaded.isPresent()) {
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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 -> JsonWriter.create(work))
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.saveAsTextFile(workingPath.concat("orcid_dataset/works"), GzipCodec.class);
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});
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.saveAsTextFile(workingPath.concat("orcid_dataset/new_works"), GzipCodec.class);
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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("errorLoadingXMLWorksFoundAcc: " + errorLoadingWorksXMLFoundAcc.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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@ -2,7 +2,7 @@
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<parameters>
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<property>
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<name>spark2MaxExecutors</name>
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<value>40</value>
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<value>50</value>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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@ -372,12 +372,17 @@ public class OrcidClientTest {
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}
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@Test
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public void testReadDownloadedWork() throws Exception {
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public void testUpdatedRecord() throws Exception {
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final String base64CompressedRecord = IOUtils
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.toString(getClass().getResourceAsStream("0000-0002-6664-7451_work.compressed.base64"));
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final String work = ArgumentApplicationParser.decompressValue(base64CompressedRecord);
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logToFile("\n\ndownloaded \n\n" + work);
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// final String downloadedRecord = testDownloadRecord("0000-0003-3028-6161", REQUEST_TYPE_RECORD);
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// assertTrue(recordFromSeqFile.equals(downloadedRecord));
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.toString(getClass().getResourceAsStream("0000-0003-3028-6161.compressed.base64"));
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final String record = ArgumentApplicationParser.decompressValue(base64CompressedRecord);
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logToFile("\n\nrecord updated \n\n" + record);
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}
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@Test
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public void testUpdatedWork() throws Exception {
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final String base64CompressedWork = "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";
|
||||
final String work = ArgumentApplicationParser.decompressValue(base64CompressedWork);
|
||||
logToFile("\n\nwork updated \n\n" + work);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
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Reference in New Issue