From 8812ab65e17de282cd3a76259a7589bae3342ad2 Mon Sep 17 00:00:00 2001 From: Enrico Ottonello Date: Fri, 4 Dec 2020 21:13:49 +0100 Subject: [PATCH] completed download function to wf; added accumulators --- .../orcid/SparkDownloadOrcidWorks.java | 190 +-- .../doiboost/orcid/xml/XMLRecordParser.java | 15 +- .../oozie_app/workflow.xml | 29 +- .../doiboost/orcid/OrcidClientTest.java | 12 +- .../orcid/xml/XMLRecordParserTest.java | 31 +- ...0000-0002-6664-7451_work.compressed.base64 | 1 + .../orcid/xml/record_0000-0001-5004-5918.xml | 1202 +++++++++++++++++ .../orcid/xml/record_8888-8888-8888-8880.xml | 2 +- 8 files changed, 1376 insertions(+), 106 deletions(-) create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0002-6664-7451_work.compressed.base64 create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/record_0000-0001-5004-5918.xml diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidWorks.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidWorks.java index ce111570a7..f67e7e0ec4 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidWorks.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidWorks.java @@ -4,12 +4,14 @@ package eu.dnetlib.doiboost.orcid; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.IOException; -import java.text.SimpleDateFormat; +import java.time.LocalDate; +import java.time.format.DateTimeFormatter; import java.util.*; -import org.apache.commons.compress.utils.Lists; 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.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpGet; @@ -17,32 +19,31 @@ import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaPairRDD; -import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.Function; import org.apache.spark.util.LongAccumulator; -import org.mortbay.log.Log; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.google.gson.JsonElement; import com.google.gson.JsonParser; -import com.ximpleware.NavException; -import com.ximpleware.ParseException; -import com.ximpleware.XPathEvalException; -import com.ximpleware.XPathParseException; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.doiboost.orcid.model.DownloadedRecordData; -import eu.dnetlib.doiboost.orcid.model.WorkData; import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser; import scala.Tuple2; public class SparkDownloadOrcidWorks { static Logger logger = LoggerFactory.getLogger(SparkDownloadOrcidWorks.class); - static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss"; - static final String lastUpdate = "2020-09-29 00:00:00"; + public static final String LAMBDA_FILE_DATE_FORMAT = "yyyy-MM-dd HH:mm:ss"; + public static final DateTimeFormatter LAMBDA_FILE_DATE_FORMATTER = DateTimeFormatter + .ofPattern(LAMBDA_FILE_DATE_FORMAT); + public static final String ORCID_XML_DATETIME_FORMAT = "yyyy-MM-dd'T'HH:mm:ss.SSS'Z'"; + public static final DateTimeFormatter ORCID_XML_DATETIMEFORMATTER = DateTimeFormatter + .ofPattern(ORCID_XML_DATETIME_FORMAT); + public static final String lastUpdateValue = "2020-09-29 00:00:00"; public static void main(String[] args) throws IOException, Exception { @@ -60,12 +61,8 @@ public class SparkDownloadOrcidWorks { logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String workingPath = parser.get("workingPath"); logger.info("workingPath: ", workingPath); -// final String outputPath = parser.get("outputPath"); - final String outputPath = "downloads/updated_works"; - logger.info("outputPath: ", outputPath); + final String outputPath = parser.get("outputPath"); final String token = parser.get("token"); -// final String lambdaFileName = parser.get("lambdaFileName"); -// logger.info("lambdaFileName: ", lambdaFileName); SparkConf conf = new SparkConf(); runWithSparkSession( @@ -73,9 +70,23 @@ public class SparkDownloadOrcidWorks { isSparkSessionManaged, spark -> { JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - LongAccumulator parsedRecordsAcc = spark.sparkContext().longAccumulator("parsed_records"); - LongAccumulator modifiedRecordsAcc = spark.sparkContext().longAccumulator("to_download_records"); + LongAccumulator updatedAuthorsAcc = spark.sparkContext().longAccumulator("updated_authors"); + LongAccumulator parsedAuthorsAcc = spark.sparkContext().longAccumulator("parsed_authors"); + LongAccumulator parsedWorksAcc = spark.sparkContext().longAccumulator("parsed_works"); + LongAccumulator modifiedWorksAcc = spark.sparkContext().longAccumulator("modified_works"); + LongAccumulator maxModifiedWorksLimitAcc = spark + .sparkContext() + .longAccumulator("max_modified_works_limit"); + LongAccumulator errorCodeFoundAcc = spark.sparkContext().longAccumulator("error_code_found"); + LongAccumulator errorLoadingJsonFoundAcc = spark + .sparkContext() + .longAccumulator("error_loading_json_found"); + LongAccumulator errorLoadingXMLFoundAcc = spark + .sparkContext() + .longAccumulator("error_loading_xml_found"); + LongAccumulator errorParsingXMLFoundAcc = spark + .sparkContext() + .longAccumulator("error_parsing_xml_found"); LongAccumulator downloadedRecordsAcc = spark.sparkContext().longAccumulator("downloaded_records"); LongAccumulator errorHTTP403Acc = spark.sparkContext().longAccumulator("error_HTTP_403"); LongAccumulator errorHTTP409Acc = spark.sparkContext().longAccumulator("error_HTTP_409"); @@ -83,38 +94,60 @@ public class SparkDownloadOrcidWorks { LongAccumulator errorHTTP525Acc = spark.sparkContext().longAccumulator("error_HTTP_525"); LongAccumulator errorHTTPGenericAcc = spark.sparkContext().longAccumulator("error_HTTP_Generic"); - logger.info("Retrieving updated authors"); JavaPairRDD updatedAuthorsRDD = sc .sequenceFile(workingPath + "downloads/updated_authors/*", Text.class, Text.class); - logger.info("Updated authors retrieved: " + updatedAuthorsRDD.count()); + updatedAuthorsAcc.setValue(updatedAuthorsRDD.count()); - Function, Iterator> retrieveWorkUrlFunction = data -> { + FlatMapFunction, String> retrieveWorkUrlFunction = data -> { String orcidId = data._1().toString(); String jsonData = data._2().toString(); - List orcidIdWorkId = Lists.newArrayList(); - Map workIdLastModifiedDate = retrieveWorkIdLastModifiedDate(jsonData); + List workIds = new ArrayList<>(); + Map workIdLastModifiedDate = new HashMap<>(); + JsonElement jElement = new JsonParser().parse(jsonData); + String statusCode = getJsonValue(jElement, "statusCode"); + if (statusCode.equals("200")) { + String compressedData = getJsonValue(jElement, "compressedData"); + if (StringUtils.isEmpty(compressedData)) { + errorLoadingJsonFoundAcc.add(1); + } else { + String authorSummary = ArgumentApplicationParser.decompressValue(compressedData); + if (StringUtils.isEmpty(authorSummary)) { + errorLoadingXMLFoundAcc.add(1); + } else { + try { + workIdLastModifiedDate = XMLRecordParser + .retrieveWorkIdLastModifiedDate(authorSummary.getBytes()); + } catch (Exception e) { + logger.error("parsing " + orcidId + " [" + jsonData + "]", e); + errorParsingXMLFoundAcc.add(1); + } + } + } + } else { + errorCodeFoundAcc.add(1); + } + parsedAuthorsAcc.add(1); workIdLastModifiedDate.forEach((k, v) -> { + parsedWorksAcc.add(1); if (isModified(orcidId, v)) { - orcidIdWorkId.add(orcidId.concat("/work/").concat(k)); + modifiedWorksAcc.add(1); + workIds.add(orcidId.concat("/work/").concat(k)); } }); - Iterator iterator = orcidIdWorkId.iterator(); - return iterator; + if (workIdLastModifiedDate.size() > 50) { + maxModifiedWorksLimitAcc.add(1); + } + return workIds.iterator(); }; - List> toDownloadWorksRDD = updatedAuthorsRDD - .map(retrieveWorkUrlFunction) - .take(1000); - sc.parallelize(toDownloadWorksRDD).saveAsTextFile(workingPath.concat("downloads/updated_works_test/")); - - Function, Tuple2> downloadRecordFunction = data -> { - String orcidId = data._1().toString(); - String lastModifiedDate = data._2().toString(); + Function> downloadWorkFunction = data -> { + String relativeWorkUrl = data; + String orcidId = relativeWorkUrl.split("/")[0]; final DownloadedRecordData downloaded = new DownloadedRecordData(); downloaded.setOrcidId(orcidId); - downloaded.setLastModifiedDate(lastModifiedDate); + downloaded.setLastModifiedDate(lastUpdateValue); try (CloseableHttpClient client = HttpClients.createDefault()) { - HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/work"); + HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + relativeWorkUrl); httpGet.addHeader("Accept", "application/vnd.orcid+xml"); httpGet.addHeader("Authorization", String.format("Bearer %s", token)); long startReq = System.currentTimeMillis(); @@ -153,62 +186,55 @@ public class SparkDownloadOrcidWorks { .compressArgument(IOUtils.toString(response.getEntity().getContent()))); } catch (Throwable e) { logger.info("Downloading " + orcidId, e.getMessage()); + if (downloaded.getStatusCode() == 503) { + throw new RuntimeException("Orcid request rate limit reached (HTTP 503)"); + } downloaded.setErrorMessage(e.getMessage()); return downloaded.toTuple2(); } return downloaded.toTuple2(); }; -// sc.hadoopConfiguration().set("mapreduce.output.fileoutputformat.compress", "true"); +// sc.hadoopConfiguration().set("mapreduce.output.fileoutputformat.compress", "true"); -// logger.info("Start downloading ..."); -// updatedAuthorsRDD -// .map(downloadRecordFunction) -// .mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2()))) -// .saveAsNewAPIHadoopFile( -// workingPath.concat(outputPath), -// Text.class, -// Text.class, -// SequenceFileOutputFormat.class, -// sc.hadoopConfiguration()); -// logger.info("parsedRecordsAcc: " + parsedRecordsAcc.value().toString()); -// logger.info("modifiedRecordsAcc: " + modifiedRecordsAcc.value().toString()); -// logger.info("downloadedRecordsAcc: " + downloadedRecordsAcc.value().toString()); -// logger.info("errorHTTP403Acc: " + errorHTTP403Acc.value().toString()); -// logger.info("errorHTTP409Acc: " + errorHTTP409Acc.value().toString()); -// logger.info("errorHTTP503Acc: " + errorHTTP503Acc.value().toString()); -// logger.info("errorHTTP525Acc: " + errorHTTP525Acc.value().toString()); -// logger.info("errorHTTPGenericAcc: " + errorHTTPGenericAcc.value().toString()); + updatedAuthorsRDD + .flatMap(retrieveWorkUrlFunction) + .repartition(100) + .map(downloadWorkFunction) + .mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2()))) + .saveAsTextFile(workingPath.concat(outputPath), GzipCodec.class); +// .saveAsNewAPIHadoopFile( +// workingPath.concat(outputPath), +// Text.class, +// Text.class, +// SequenceFileOutputFormat.class, +// sc.hadoopConfiguration()); + logger.info("updatedAuthorsAcc: " + updatedAuthorsAcc.value().toString()); + logger.info("parsedAuthorsAcc: " + parsedAuthorsAcc.value().toString()); + logger.info("parsedWorksAcc: " + parsedWorksAcc.value().toString()); + logger.info("modifiedWorksAcc: " + modifiedWorksAcc.value().toString()); + logger.info("maxModifiedWorksLimitAcc: " + maxModifiedWorksLimitAcc.value().toString()); + logger.info("errorCodeFoundAcc: " + errorCodeFoundAcc.value().toString()); + logger.info("errorLoadingJsonFoundAcc: " + errorLoadingJsonFoundAcc.value().toString()); + logger.info("errorLoadingXMLFoundAcc: " + errorLoadingXMLFoundAcc.value().toString()); + logger.info("errorParsingXMLFoundAcc: " + errorParsingXMLFoundAcc.value().toString()); + logger.info("downloadedRecordsAcc: " + downloadedRecordsAcc.value().toString()); + logger.info("errorHTTP403Acc: " + errorHTTP403Acc.value().toString()); + logger.info("errorHTTP409Acc: " + errorHTTP409Acc.value().toString()); + logger.info("errorHTTP503Acc: " + errorHTTP503Acc.value().toString()); + logger.info("errorHTTP525Acc: " + errorHTTP525Acc.value().toString()); + logger.info("errorHTTPGenericAcc: " + errorHTTPGenericAcc.value().toString()); }); } - private static boolean isModified(String orcidId, String modifiedDate) { - Date modifiedDateDt = null; - Date lastUpdateDt = null; - try { - if (modifiedDate.length() != 19) { - modifiedDate = modifiedDate.substring(0, 19); - } - modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate); - lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate); - } catch (Exception e) { - logger.info("[" + orcidId + "] Parsing date: ", e.getMessage()); - return true; - } - return modifiedDateDt.after(lastUpdateDt); - } - - private static Map retrieveWorkIdLastModifiedDate(String json) - throws XPathEvalException, NavException, XPathParseException, ParseException { - JsonElement jElement = new JsonParser().parse(json); - String statusCode = getJsonValue(jElement, "statusCode"); - if (statusCode.equals("200")) { - String compressedData = getJsonValue(jElement, "compressedData"); - String authorSummary = ArgumentApplicationParser.decompressValue(compressedData); - return XMLRecordParser.retrieveWorkIdLastModifiedDate(authorSummary.getBytes()); - } - return new HashMap<>(); + public static boolean isModified(String orcidId, String modifiedDateValue) { + LocalDate modifiedDate = null; + LocalDate lastUpdate = null; + modifiedDate = LocalDate.parse(modifiedDateValue, SparkDownloadOrcidWorks.ORCID_XML_DATETIMEFORMATTER); + lastUpdate = LocalDate + .parse(SparkDownloadOrcidWorks.lastUpdateValue, SparkDownloadOrcidWorks.LAMBDA_FILE_DATE_FORMATTER); + return modifiedDate.isAfter(lastUpdate); } private static String getJsonValue(JsonElement jElement, String property) { diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java index 5accb561d0..8787a8dd28 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java @@ -1,6 +1,7 @@ package eu.dnetlib.doiboost.orcid.xml; +import java.io.IOException; import java.util.*; import org.mortbay.log.Log; @@ -161,30 +162,22 @@ public class XMLRecordParser { } public static Map retrieveWorkIdLastModifiedDate(byte[] bytes) - throws ParseException, XPathParseException, NavException, XPathEvalException { + throws ParseException, XPathParseException, NavException, XPathEvalException, IOException { final VTDGen vg = new VTDGen(); vg.setDoc(bytes); vg.parse(true); final VTDNav vn = vg.getNav(); final AutoPilot ap = new AutoPilot(vn); - ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL); - ap.declareXPathNameSpace(NS_PERSON, NS_PERSON_URL); - ap.declareXPathNameSpace(NS_DETAILS, NS_DETAILS_URL); - ap.declareXPathNameSpace(NS_OTHER, NS_OTHER_URL); - ap.declareXPathNameSpace(NS_RECORD, NS_RECORD_URL); - ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL); ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL); - ap.declareXPathNameSpace(NS_ACTIVITIES, NS_ACTIVITIES_URL); + ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL); Map workIdLastModifiedDate = new HashMap<>(); ap.selectXPath("//work:work-summary"); - + String workId = ""; while (ap.evalXPath() != -1) { - String workId = ""; String lastModifiedDate = ""; int attr = vn.getAttrVal("put-code"); if (attr > -1) { workId = vn.toNormalizedString(attr); - workIdLastModifiedDate.put(workId, ""); } if (vn.toElement(VTDNav.FIRST_CHILD, "common:last-modified-date")) { int val = vn.getText(); diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml index b9383558cc..8844a15391 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_updates_download/oozie_app/workflow.xml @@ -66,7 +66,7 @@ - + @@ -163,6 +163,33 @@ + + + + yarn-cluster + cluster + DownloadOrcidWorks + eu.dnetlib.doiboost.orcid.SparkDownloadOrcidWorks + dhp-doiboost-${projectVersion}.jar + + --conf spark.dynamicAllocation.enabled=true + --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + + -w${workingPath}/ + -n${nameNode} + -f- + -odownloads/updated_works + -t${token} + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java index fc18132a15..67dc9f5c48 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java @@ -344,7 +344,7 @@ public class OrcidClientTest { } @Test - public void cleanAuthorListTest() throws Exception { + private void cleanAuthorListTest() throws Exception { AuthorData a1 = new AuthorData(); a1.setOid("1"); a1.setName("n1"); @@ -370,4 +370,14 @@ public class OrcidClientTest { list.removeIf(a -> !namesAlreadySeen.add(a.getOid())); assertTrue(list.size() == 2); } + + @Test + public void testReadDownloadedWork() throws Exception { + final String base64CompressedRecord = IOUtils + .toString(getClass().getResourceAsStream("0000-0002-6664-7451_work.compressed.base64")); + final String work = ArgumentApplicationParser.decompressValue(base64CompressedRecord); + logToFile("\n\ndownloaded \n\n" + work); +// final String downloadedRecord = testDownloadRecord("0000-0003-3028-6161", REQUEST_TYPE_RECORD); +// assertTrue(recordFromSeqFile.equals(downloadedRecord)); + } } diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java index 7dc42deb85..aeb9400a6a 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java @@ -4,17 +4,27 @@ package eu.dnetlib.doiboost.orcid.xml; import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertTrue; +import java.io.IOException; +import java.time.LocalDate; +import java.util.HashMap; import java.util.Map; import org.apache.commons.io.IOUtils; import org.junit.jupiter.api.Test; +import com.ximpleware.*; + import eu.dnetlib.dhp.schema.orcid.AuthorData; import eu.dnetlib.doiboost.orcid.OrcidClientTest; +import eu.dnetlib.doiboost.orcid.SparkDownloadOrcidWorks; import eu.dnetlib.doiboost.orcid.model.WorkData; import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter; public class XMLRecordParserTest { + private static final String NS_WORK = "work"; + private static final String NS_WORK_URL = "http://www.orcid.org/ns/work"; + private static final String NS_COMMON_URL = "http://www.orcid.org/ns/common"; + private static final String NS_COMMON = "common"; @Test private void testOrcidAuthorDataXMLParser() throws Exception { @@ -67,9 +77,6 @@ public class XMLRecordParserTest { String xml = IOUtils .toString( this.getClass().getResourceAsStream("summary_0000-0001-5109-1000_othername.xml")); - - XMLRecordParser p = new XMLRecordParser(); - AuthorData authorData = XMLRecordParser.VTDParseAuthorData(xml.getBytes()); assertNotNull(authorData); assertNotNull(authorData.getOtherNames()); @@ -80,14 +87,18 @@ public class XMLRecordParserTest { @Test public void testWorkIdLastModifiedDateXMLParser() throws Exception { - String xml = IOUtils .toString( - this.getClass().getResourceAsStream("record_8888-8888-8888-8880.xml")); -// Map workIdLastModifiedDate = XMLRecordParser.retrieveWorkIdLastModifiedDate(xml.getBytes()); -// String LastModifiedDate = workIdLastModifiedDate.get(0); -// OrcidClientTest.logToFile(LastModifiedDate + " -- " + workIdLastModifiedDate.get(LastModifiedDate)); - String result = XMLRecordParser.retrieveWorkIdFromSummary(xml.getBytes(), "empty"); - OrcidClientTest.logToFile(result); + this.getClass().getResourceAsStream("record_0000-0001-5004-5918.xml")); + Map workIdLastModifiedDate = XMLRecordParser.retrieveWorkIdLastModifiedDate(xml.getBytes()); + workIdLastModifiedDate.forEach((k, v) -> { + try { + OrcidClientTest + .logToFile( + k + " " + v + " isModified after " + SparkDownloadOrcidWorks.lastUpdateValue + ": " + + SparkDownloadOrcidWorks.isModified("0000-0001-5004-5918", v)); + } catch (IOException e) { + } + }); } } diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0002-6664-7451_work.compressed.base64 b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0002-6664-7451_work.compressed.base64 new file mode 100644 index 0000000000..7e5a73b73d --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/0000-0002-6664-7451_work.compressed.base64 @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/record_0000-0001-5004-5918.xml b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/record_0000-0001-5004-5918.xml new file mode 100644 index 0000000000..9534686aed --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/record_0000-0001-5004-5918.xml @@ -0,0 +1,1202 @@ + + + + https://orcid.org/0000-0001-5004-5918 + 0000-0001-5004-5918 + orcid.org + + + en + + + Direct + 2016-11-06T20:12:32.296Z + 2020-04-23T07:30:59.917Z + true + false + false + + + 2017-01-04T07:46:27.991Z + + 2016-11-06T20:12:32.525Z + 2016-11-06T20:12:32.525Z + Aurélie + Prémaud + + + + + + + + 2017-01-04T07:46:27.991Z + + 2017-01-04T07:46:27.991Z + 2017-01-04T07:46:27.991Z + + + https://orcid.org/client/0000-0003-1377-5676 + 0000-0003-1377-5676 + orcid.org + + ResearcherID + + https://orcid.org/0000-0001-5004-5918 + 0000-0001-5004-5918 + orcid.org + + Aurélie Prémaud + + ResearcherID + A-2095-2017 + http://www.researcherid.com/rid/A-2095-2017 + self + + + + + 2019-04-08T23:37:26.263Z + + + + + + + + + + + + 2019-04-08T23:37:26.263Z + + 2019-04-08T23:37:26.263Z + + + doi + 10.1155/2019/7245142 + 10.1155/2019/7245142 + https://doi.org/10.1155/2019/7245142 + self + + + + 2019-04-08T23:37:26.263Z + 2019-04-08T23:37:26.263Z + + + https://orcid.org/client/0000-0001-9884-1913 + 0000-0001-9884-1913 + orcid.org + + Crossref + + + A Prognostic Tool for Individualized Prediction of Graft Failure Risk within Ten Years after Kidney Transplantation + + + + doi + 10.1155/2019/7245142 + 10.1155/2019/7245142 + https://doi.org/10.1155/2019/7245142 + self + + + https://doi.org/10.1155/2019/7245142 + journal-article + + 2019 + 04 + 08 + + Journal of Transplantation + + + + 2018-10-03T15:11:13.783Z + + + doi + 10.1371/journal.pone.0180236 + 10.1371/journal.pone.0180236 + https://doi.org/10.1371/journal.pone.0180236 + self + + + + 2020-11-30T01:02:03.444Z + 2020-11-30T01:02:03.444Z + + + https://orcid.org/client/0000-0001-9884-1913 + 0000-0001-9884-1913 + orcid.org + + Crossref + + + An adjustable predictive score of graft survival in kidney transplant patients and the levels of risk linked to de novo donor-specific anti-HLA antibodies + + + + doi + 10.1371/journal.pone.0180236 + 10.1371/journal.pone.0180236 + https://doi.org/10.1371/journal.pone.0180236 + self + + + https://doi.org/10.1371/journal.pone.0180236 + journal-article + + 2017 + 07 + 03 + + PLOS ONE + + + + 2018-08-23T12:01:11.624Z + + + doi + 10.1038/clpt.2014.140 + 10.1038/clpt.2014.140 + self + + + wosuid + WOS:000342675400030 + wos:000342675400030 + self + + + + 2018-08-23T12:01:11.624Z + 2018-08-23T12:01:11.624Z + + + https://orcid.org/client/0000-0003-1377-5676 + 0000-0003-1377-5676 + orcid.org + + ResearcherID + + https://orcid.org/0000-0001-5004-5918 + 0000-0001-5004-5918 + orcid.org + + Aurélie Prémaud + + + Exposure to mycophenolic acid better predicts immunosuppressive efficacy than exposure to calcineurin inhibitors in renal transplant patients + + + + doi + 10.1038/clpt.2014.140 + 10.1038/clpt.2014.140 + self + + + wosuid + WOS:000342675400030 + wos:000342675400030 + self + + + http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000342675400030&KeyUID=WOS:000342675400030 + journal-article + + 2014 + + Clinical Pharmacology and Therapeutics + + + + 2018-08-23T12:01:11.635Z + + + wosuid + WOS:000336395700020 + wos:000336395700020 + self + + + doi + 10.1007/s00280-014-2466-0 + 10.1007/s00280-014-2466-0 + self + + + + 2018-08-23T12:01:11.635Z + 2018-08-23T12:01:11.635Z + + + https://orcid.org/client/0000-0003-1377-5676 + 0000-0003-1377-5676 + orcid.org + + ResearcherID + + https://orcid.org/0000-0001-5004-5918 + 0000-0001-5004-5918 + orcid.org + + Aurélie Prémaud + + + Pharmacokinetics and exposure-effect relationships of capecitabine in elderly patients with breast or colorectal cancer + + + + doi + 10.1007/s00280-014-2466-0 + 10.1007/s00280-014-2466-0 + self + + + wosuid + WOS:000336395700020 + wos:000336395700020 + self + + + http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000336395700020&KeyUID=WOS:000336395700020 + journal-article + + 2014 + + Cancer Chemotherapy and Pharmacology + + + + 2018-08-23T12:01:11.639Z + + + doi + 10.1007/s40262-013-0037-x + 10.1007/s40262-013-0037-x + self + + + wosuid + WOS:000318524800005 + wos:000318524800005 + self + + + + 2018-08-23T12:01:11.639Z + 2018-08-23T12:01:11.639Z + + + https://orcid.org/client/0000-0003-1377-5676 + 0000-0003-1377-5676 + orcid.org + + ResearcherID + + https://orcid.org/0000-0001-5004-5918 + 0000-0001-5004-5918 + orcid.org + + Aurélie Prémaud + + + Ciclosporin population pharmacokinetics and Bayesian estimation in thoracic transplant recipients + + + + doi + 10.1007/s40262-013-0037-x + 10.1007/s40262-013-0037-x + self + + + wosuid + WOS:000318524800005 + wos:000318524800005 + self + + + http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000318524800005&KeyUID=WOS:000318524800005 + journal-article + + 2013 + + Clinical Pharmacokinetics + + + + 2018-08-23T12:01:11.643Z + + + doi + 10.1016/j.phrs.2013.03.009 + 10.1016/j.phrs.2013.03.009 + self + + + wosuid + WOS:000319645300006 + wos:000319645300006 + self + + + + 2018-08-23T12:01:11.643Z + 2018-08-23T12:01:11.643Z + + + https://orcid.org/client/0000-0003-1377-5676 + 0000-0003-1377-5676 + orcid.org + + ResearcherID + + https://orcid.org/0000-0001-5004-5918 + 0000-0001-5004-5918 + orcid.org + + Aurélie Prémaud + + + Impact of longitudinal exposure to mycophenolic acid on acute rejection in renal-transplant recipients using a joint modeling approach + + + + doi + 10.1016/j.phrs.2013.03.009 + 10.1016/j.phrs.2013.03.009 + self + + + wosuid + WOS:000319645300006 + wos:000319645300006 + self + + + http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000319645300006&KeyUID=WOS:000319645300006 + journal-article + + 2013 + + Pharmacological Research + + + + 2018-08-23T12:01:11.646Z + + + doi + 10.2165/11594050-000000000-00000 + 10.2165/11594050-000000000-00000 + self + + + + 2018-08-23T12:01:11.646Z + 2018-08-23T12:01:11.646Z + + + https://orcid.org/client/0000-0003-1377-5676 + 0000-0003-1377-5676 + orcid.org + + ResearcherID + + https://orcid.org/0000-0001-5004-5918 + 0000-0001-5004-5918 + orcid.org + + Aurélie Prémaud + + + Bayesian estimation of mycophenolate mofetil in lung transplantation, using a population pharmacokinetic model developed in kidney and lung transplant recipients + + + + doi + 10.2165/11594050-000000000-00000 + 10.2165/11594050-000000000-00000 + self + + + http://www.ncbi.nlm.nih.gov/pubmed/22054177 + journal-article + + 2012 + + Clinical Pharmacokinetics + + + + 2018-08-23T12:01:11.650Z + + + doi + 10.1016/j.phrs.2011.01.005 + 10.1016/j.phrs.2011.01.005 + self + + + wosuid + WOS:000290892300011 + wos:000290892300011 + self + + + + 2018-08-23T12:01:11.650Z + 2018-08-23T12:01:11.650Z + + + https://orcid.org/client/0000-0003-1377-5676 + 0000-0003-1377-5676 + orcid.org + + ResearcherID + + https://orcid.org/0000-0001-5004-5918 + 0000-0001-5004-5918 + orcid.org + + Aurélie Prémaud + + + Inhibition of T-cell activation and proliferation by mycophenolic acid in patients awaiting liver transplantation: PK/PD relationships + + + + doi + 10.1016/j.phrs.2011.01.005 + 10.1016/j.phrs.2011.01.005 + self + + + wosuid + WOS:000290892300011 + wos:000290892300011 + self + + + 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