From 0386f3638592766ac5b8972afcd23292d5c372a5 Mon Sep 17 00:00:00 2001 From: "sandro.labruzzo" Date: Thu, 25 Jan 2024 19:40:59 +0100 Subject: [PATCH] Added workflow to update ORCID and replaced some parsing, because the update works and employments xml differs from the dump one. --- .../dhp/collection/orcid/OrcidParser.java | 185 +- .../dhp/collection/orcid/model/Author.java | 10 + .../orcid/apply_orcid_table_parameter.json | 26 + .../orcid/generate_orcid_table_parameter.json | 6 + .../orcid/update/oozie_app/workflow.xml | 41 +- .../collection/orcid/SparkApplyUpdate.scala | 75 + .../orcid/SparkGenerateORCIDTable.scala | 91 +- .../collection/orcid/DownloadORCIDTest.java | 37 +- .../dnetlib/dhp/collection/orcid/summary2.xml | 966 +++ .../collection/orcid/update_employments.xml | 60 + .../dhp/collection/orcid/update_work.xml | 6234 +++++++++++++++++ 11 files changed, 7684 insertions(+), 47 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/apply_orcid_table_parameter.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkApplyUpdate.scala create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/summary2.xml create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/update_employments.xml create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/update_work.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java index 159b8a5fc..ea108821e 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java @@ -1,11 +1,15 @@ package eu.dnetlib.dhp.collection.orcid; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; +import java.util.*; +import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; +import org.dom4j.Document; +import org.dom4j.DocumentFactory; +import org.dom4j.DocumentHelper; +import org.dom4j.Node; +import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -40,8 +44,8 @@ public class OrcidParser { private static final String NS_ERROR = "error"; private static final String NS_HISTORY = "history"; private static final String NS_HISTORY_URL = "http://www.orcid.org/ns/history"; - private static final String NS_BULK_URL = "http://www.orcid.org/ns/bulk"; - private static final String NS_BULK = "bulk"; + private static final String NS_EMPLOYMENT = "employment"; + private static final String NS_EMPLOYMENT_URL = "http://www.orcid.org/ns/employment"; private static final String NS_EXTERNAL = "external-identifier"; private static final String NS_EXTERNAL_URL = "http://www.orcid.org/ns/external-identifier"; @@ -61,6 +65,7 @@ public class OrcidParser { ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL); ap.declareXPathNameSpace(NS_EXTERNAL, NS_EXTERNAL_URL); ap.declareXPathNameSpace(NS_ACTIVITIES, NS_ACTIVITIES_URL); + ap.declareXPathNameSpace(NS_EMPLOYMENT, NS_EMPLOYMENT_URL); } public Author parseSummary(final String xml) { @@ -70,13 +75,15 @@ public class OrcidParser { generateParsedDocument(xml); List recordNodes = VtdUtilityParser .getTextValuesWithAttributes( - ap, vn, "//record:record", Arrays.asList("path")); + ap, vn, "//record:record", Collections.singletonList("path")); if (!recordNodes.isEmpty()) { final String oid = (recordNodes.get(0).getAttributes().get("path")).substring(1); author.setOrcid(oid); } else { return null; } + final String ltm = VtdUtilityParser.getSingleValue(ap, vn, "//common:last-modified-date"); + author.setLastModifiedDate(ltm); List personNodes = VtdUtilityParser .getTextValuesWithAttributes( ap, vn, "//person:name", Arrays.asList("visibility")); @@ -129,6 +136,64 @@ public class OrcidParser { } } + public List parseWorks(final String xml) { + + try { + String oid; + + generateParsedDocument(xml); + List workNodes = VtdUtilityParser + .getTextValuesWithAttributes(ap, vn, "//activities:works", Arrays.asList("path", "visibility")); + if (!workNodes.isEmpty()) { + oid = (workNodes.get(0).getAttributes().get("path")).split("/")[1]; + + } else { + return null; + } + final List works = new ArrayList<>(); + ap.selectXPath("//work:work-summary"); + + while (ap.evalXPath() != -1) { + final Work work = new Work(); + work.setOrcid(oid); + final AutoPilot ap1 = new AutoPilot(ap.getNav()); + ap1.selectXPath("./work:title/common:title"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + work.setTitle(vn.toNormalizedString(it)); + } + ap1.selectXPath(".//common:external-id"); + while (ap1.evalXPath() != -1) { + final Pid pid = new Pid(); + + final AutoPilot ap2 = new AutoPilot(ap1.getNav()); + + ap2.selectXPath("./common:external-id-type"); + while (ap2.evalXPath() != -1) { + int it = vn.getText(); + pid.setSchema(vn.toNormalizedString(it)); + } + ap2.selectXPath("./common:external-id-value"); + while (ap2.evalXPath() != -1) { + int it = vn.getText(); + pid.setValue(vn.toNormalizedString(it)); + } + + work.addPid(pid); + } + + works.add(work); + } + return works; + + } catch (Throwable e) { + log.error("Error on parsing {}", xml); + log.error(e.getMessage()); + return null; + } + + } + public Work parseWork(final String xml) { try { @@ -176,11 +241,15 @@ public class OrcidParser { } private String extractEmploymentDate(final String xpath) throws Exception { + return extractEmploymentDate(xpath, ap); + } - ap.selectXPath(xpath); + private String extractEmploymentDate(final String xpath, AutoPilot pp) throws Exception { + + pp.selectXPath(xpath); StringBuilder sb = new StringBuilder(); - while (ap.evalXPath() != -1) { - final AutoPilot ap1 = new AutoPilot(ap.getNav()); + while (pp.evalXPath() != -1) { + final AutoPilot ap1 = new AutoPilot(pp.getNav()); ap1.selectXPath("./common:year"); while (ap1.evalXPath() != -1) { int it = vn.getText(); @@ -203,6 +272,104 @@ public class OrcidParser { } + public List parseEmployments(final String xml) { + try { + String oid; + Map nsContext = getNameSpaceMap(); + DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); + Document doc = DocumentHelper.parseText(xml); + oid = doc.valueOf("//activities:employments/@path"); + if (oid == null || StringUtils.isEmpty(oid)) + return null; + final String orcid = oid.split("/")[1]; + + List nodes = doc.selectNodes("//employment:employment-summary"); + return nodes.stream().map(n -> { + final Employment e = new Employment(); + e.setOrcid(orcid); + + final String depName = n.valueOf(".//common:department-name"); + if (StringUtils.isNotBlank(depName)) + e.setDepartmentName(depName); + final String roleTitle = n.valueOf(".//common:role-title"); + e.setRoleTitle(roleTitle); + final String organizationName = n.valueOf(".//common:organization/common:name"); + if (StringUtils.isEmpty(e.getDepartmentName())) + e.setDepartmentName(organizationName); + final Pid p = new Pid(); + final String pid = n + .valueOf( + "./common:organization/common:disambiguated-organization/common:disambiguated-organization-identifier"); + p.setValue(pid); + final String pidType = n + .valueOf("./common:organization/common:disambiguated-organization/common:disambiguation-source"); + p.setSchema(pidType); + e.setAffiliationId(p); + + final StringBuilder aDate = new StringBuilder(); + final String sy = n.valueOf("./common:start-date/common:year"); + if (StringUtils.isNotBlank(sy)) { + aDate.append(sy); + final String sm = n.valueOf("./common:start-date/common:month"); + final String sd = n.valueOf("./common:start-date/common:day"); + aDate.append("-"); + if (StringUtils.isNotBlank(sm)) + aDate.append(sm); + else + aDate.append("01"); + aDate.append("-"); + if (StringUtils.isNotBlank(sd)) + aDate.append(sd); + else + aDate.append("01"); + e.setEndDate(aDate.toString()); + } + + final String ey = n.valueOf("./common:end-date/common:year"); + if (StringUtils.isNotBlank(ey)) { + aDate.append(ey); + final String em = n.valueOf("./common:end-date/common:month"); + final String ed = n.valueOf("./common:end-date/common:day"); + aDate.append("-"); + if (StringUtils.isNotBlank(em)) + aDate.append(em); + else + aDate.append("01"); + aDate.append("-"); + if (StringUtils.isNotBlank(ed)) + aDate.append(ed); + else + aDate.append("01"); + e.setEndDate(aDate.toString()); + } + + return e; + + }).collect(Collectors.toList()); + } catch (Throwable e) { + log.error("Error on parsing {}", xml); + log.error(e.getMessage()); + return null; + } + } + + @NotNull + private static Map getNameSpaceMap() { + Map nsContext = new HashMap<>(); + nsContext.put(NS_COMMON, NS_COMMON_URL); + nsContext.put(NS_PERSON, NS_PERSON_URL); + nsContext.put(NS_DETAILS, NS_DETAILS_URL); + nsContext.put(NS_OTHER, NS_OTHER_URL); + nsContext.put(NS_RECORD, NS_RECORD_URL); + nsContext.put(NS_ERROR, NS_ERROR_URL); + nsContext.put(NS_HISTORY, NS_HISTORY_URL); + nsContext.put(NS_WORK, NS_WORK_URL); + nsContext.put(NS_EXTERNAL, NS_EXTERNAL_URL); + nsContext.put(NS_ACTIVITIES, NS_ACTIVITIES_URL); + nsContext.put(NS_EMPLOYMENT, NS_EMPLOYMENT_URL); + return nsContext; + } + public Employment parseEmployment(final String xml) { try { final Employment employment = new Employment(); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java index 32c321b41..df87e4333 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java @@ -18,6 +18,8 @@ public class Author extends ORCIDItem { private String biography; + private String lastModifiedDate; + public String getBiography() { return biography; } @@ -74,6 +76,14 @@ public class Author extends ORCIDItem { this.otherPids = otherPids; } + public String getLastModifiedDate() { + return lastModifiedDate; + } + + public void setLastModifiedDate(String lastModifiedDate) { + this.lastModifiedDate = lastModifiedDate; + } + public void addOtherPid(final Pid pid) { if (otherPids == null) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/apply_orcid_table_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/apply_orcid_table_parameter.json new file mode 100644 index 000000000..3d3374c74 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/apply_orcid_table_parameter.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "the master name", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target PATH of the DF tables", + "paramRequired": true + }, + { + "paramName": "g", + "paramLongName": "graphPath", + "paramDescription": "the PATH of the current graph path", + "paramRequired": true + }, + { + "paramName": "u", + "paramLongName": "updatePath", + "paramDescription": "the PATH of the current graph update path", + "paramRequired": true + } + ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json index 01d81ea97..d088e8c77 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json @@ -16,6 +16,12 @@ "paramLongName": "sourcePath", "paramDescription": "the PATH of the ORCID sequence file", "paramRequired": true + }, + { + "paramName": "fu", + "paramLongName": "fromUpdate", + "paramDescription": "whether we have to generate table from dump or from update", + "paramRequired": false } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/workflow.xml index d7a81b022..434d21a0c 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/workflow.xml @@ -1,5 +1,9 @@ + + graphPath + the path to store the original ORCID dump + targetPath the path to store the original ORCID dump @@ -12,8 +16,9 @@ accessToken The access token - + + @@ -37,7 +42,7 @@ --accessToken${accessToken} - + @@ -58,8 +63,36 @@ --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --sourcePath${targetPath}/extracted - --targetPath${targetPath}/tables + --sourcePath${targetPath} + --targetPath${targetPath}/updateTable + --fromUpdatetrue + --masteryarn + + + + + + + + yarn + cluster + Update ORCID Tables + eu.dnetlib.dhp.collection.orcid.SparkApplyUpdate + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.executor.memoryOverhead=2g + --conf spark.sql.shuffle.partitions=3000 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --graphPathgraphPath + --updatePath${targetPath}/updateTable + --targetPath${targetPath}/newTable --masteryarn diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkApplyUpdate.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkApplyUpdate.scala new file mode 100644 index 000000000..4494a2d3d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkApplyUpdate.scala @@ -0,0 +1,75 @@ +package eu.dnetlib.dhp.collection.orcid + +import eu.dnetlib.dhp.application.AbstractScalaApplication +import org.apache.spark.sql.{DataFrame, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +class SparkApplyUpdate(propertyPath: String, args: Array[String], log: Logger) + extends AbstractScalaApplication(propertyPath, args, log: Logger) { + + /** Here all the spark applications runs this method + * where the whole logic of the spark node is defined + */ + override def run(): Unit = { + + val graphPath: String = parser.get("graphPath") + log.info("found parameters graphPath: {}", graphPath) + val updatePath: String = parser.get("updatePath") + log.info("found parameters updatePath: {}", updatePath) + val targetPath: String = parser.get("targetPath") + log.info("found parameters targetPath: {}", targetPath) + applyTableUpdate(spark, graphPath, updatePath, targetPath) + + } + + def updateDataset( + inputDataset: DataFrame, + idUpdate: DataFrame, + updateDataframe: DataFrame, + targetPath: String + ): Unit = { + inputDataset + .join(idUpdate, inputDataset("orcid").equalTo(idUpdate("orcid")), "leftanti") + .select(inputDataset("*")) + .unionByName(updateDataframe) + .write + .mode(SaveMode.Overwrite) + .save(targetPath) + } + + def applyTableUpdate(spark: SparkSession, graphPath: String, updatePath: String, targetPath: String) = { + val orcidIDUpdate = spark.read.load(s"$updatePath/Authors").select("orcid") + updateDataset( + spark.read.load(s"$graphPath/Authors"), + orcidIDUpdate, + spark.read.load(s"$updatePath/Authors"), + s"$targetPath/Authors" + ) + updateDataset( + spark.read.load(s"$graphPath/Employments"), + orcidIDUpdate, + spark.read.load(s"$updatePath/Employments"), + s"$targetPath/Employments" + ) + updateDataset( + spark.read.load(s"$graphPath/Works"), + orcidIDUpdate, + spark.read.load(s"$updatePath/Works"), + s"$targetPath/Works" + ) + } + +} + +object SparkApplyUpdate { + + val log: Logger = LoggerFactory.getLogger(SparkGenerateORCIDTable.getClass) + + def main(args: Array[String]): Unit = { + + new SparkApplyUpdate("/eu/dnetlib/dhp/collection/orcid/apply_orcid_table_parameter.json", args, log) + .initialize() + .run() + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala index f0c4cd214..4f617f15c 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala @@ -6,6 +6,7 @@ import org.apache.hadoop.io.Text import org.apache.spark.SparkContext import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} +import scala.collection.JavaConverters._ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Logger) extends AbstractScalaApplication(propertyPath, args, log: Logger) { @@ -18,12 +19,16 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo log.info("found parameters sourcePath: {}", sourcePath) val targetPath: String = parser.get("targetPath") log.info("found parameters targetPath: {}", targetPath) - extractORCIDTable(spark, sourcePath, targetPath) - extractORCIDEmploymentsTable(spark, sourcePath, targetPath) - extractORCIDWorksTable(spark, sourcePath, targetPath) + val fromUpdate = "true".equals(parser.get("fromUpdate")) + val sourceSummaryPath = if (fromUpdate) s"$sourcePath/summary*" else sourcePath + val sourceEmploymentsPath = if (fromUpdate) s"$sourcePath/employments*" else sourcePath + val sourceWorksPath = if (fromUpdate) s"$sourcePath/works*" else sourcePath + extractORCIDTable(spark, sourceSummaryPath, targetPath, fromUpdate) + extractORCIDEmploymentsTable(spark, sourceEmploymentsPath, targetPath, fromUpdate) + extractORCIDWorksTable(spark, sourceWorksPath, targetPath, fromUpdate) } - def extractORCIDTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = { + def extractORCIDTable(spark: SparkSession, sourcePath: String, targetPath: String, skipFilterByKey: Boolean): Unit = { val sc: SparkContext = spark.sparkContext import spark.implicits._ val df = sc @@ -32,8 +37,8 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo .toDF .as[(String, String)] implicit val orcidAuthor: Encoder[Author] = Encoders.bean(classOf[Author]) -// implicit val orcidPID:Encoder[Pid] = Encoders.bean(classOf[Pid]) - df.filter(r => r._1.contains("summaries")) + val newDf = if (!skipFilterByKey) df.filter(r => r._1.contains("summaries")) else df + newDf .map { r => val p = new OrcidParser p.parseSummary(r._2) @@ -44,7 +49,12 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo .save(s"$targetPath/Authors") } - def extractORCIDWorksTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = { + def extractORCIDWorksTable( + spark: SparkSession, + sourcePath: String, + targetPath: String, + skipFilterByKey: Boolean + ): Unit = { val sc: SparkContext = spark.sparkContext import spark.implicits._ val df = sc @@ -53,19 +63,37 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo .toDF .as[(String, String)] implicit val orcidWorkAuthor: Encoder[Work] = Encoders.bean(classOf[Work]) - implicit val orcidPID: Encoder[Pid] = Encoders.bean(classOf[Pid]) - df.filter(r => r._1.contains("works")) - .map { r => + + //We are in the case of parsing ORCID UPDATE + if (skipFilterByKey) { + df.flatMap { r => val p = new OrcidParser - p.parseWork(r._2) - } - .filter(p => p != null) - .write - .mode(SaveMode.Overwrite) - .save(s"$targetPath/Works") + p.parseWorks(r._2).asScala + }.filter(p => p != null) + .write + .mode(SaveMode.Overwrite) + .save(s"$targetPath/Works") + } + //We are in the case of parsing ORCID DUMP + else { + df.filter(r => r._1.contains("works")) + .map { r => + val p = new OrcidParser + p.parseWork(r._2) + } + .filter(p => p != null) + .write + .mode(SaveMode.Overwrite) + .save(s"$targetPath/Works") + } } - def extractORCIDEmploymentsTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = { + def extractORCIDEmploymentsTable( + spark: SparkSession, + sourcePath: String, + targetPath: String, + skipFilterByKey: Boolean + ): Unit = { val sc: SparkContext = spark.sparkContext import spark.implicits._ val df = sc @@ -74,16 +102,27 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo .toDF .as[(String, String)] implicit val orcidEmploymentAuthor: Encoder[Employment] = Encoders.bean(classOf[Employment]) - implicit val orcidPID: Encoder[Pid] = Encoders.bean(classOf[Pid]) - df.filter(r => r._1.contains("employments")) - .map { r => + if (skipFilterByKey) { + df.flatMap { r => val p = new OrcidParser - p.parseEmployment(r._2) - } - .filter(p => p != null) - .write - .mode(SaveMode.Overwrite) - .save(s"$targetPath/Employments") + p.parseEmployments(r._2).asScala + }.filter(p => p != null) + .write + .mode(SaveMode.Overwrite) + .save(s"$targetPath/Employments") + } + //We are in the case of parsing ORCID DUMP + else { + df.filter(r => r._1.contains("employments")) + .map { r => + val p = new OrcidParser + p.parseEmployment(r._2) + } + .filter(p => p != null) + .write + .mode(SaveMode.Overwrite) + .save(s"$targetPath/Employments") + } } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java index 846282721..f42d1d875 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java @@ -33,6 +33,7 @@ import com.ximpleware.XPathParseException; import eu.dnetlib.dhp.collection.orcid.model.Author; import eu.dnetlib.dhp.collection.orcid.model.ORCIDItem; +import eu.dnetlib.dhp.collection.orcid.model.Work; import eu.dnetlib.dhp.parser.utility.VtdException; public class DownloadORCIDTest { @@ -88,6 +89,34 @@ public class DownloadORCIDTest { }); } + @Test + public void testParsingOrcidUpdateEmployments() throws Exception { + final String xml = IOUtils + .toString( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/orcid/update_employments.xml"))); + + final OrcidParser parser = new OrcidParser(); + final ObjectMapper mapper = new ObjectMapper(); + System.out.println(mapper.writeValueAsString(parser.parseEmployments(xml))); + } + + @Test + public void testParsingOrcidUpdateWorks() throws Exception { + final String xml = IOUtils + .toString( + Objects + .requireNonNull( + getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/orcid/update_work.xml"))); + + final OrcidParser parser = new OrcidParser(); + final List works = parser.parseWorks(xml); + + final ObjectMapper mapper = new ObjectMapper(); + System.out.println(mapper.writeValueAsString(works)); + } + @Test public void testParsingEmployments() throws Exception { @@ -122,12 +151,4 @@ public class DownloadORCIDTest { }); } -// @Test -// public void testReadTar() throws Exception { -// OrcidGetUpdatesFile.main(new String[] { -// "--namenode", "puppa" -// }); -// -// } - } diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/summary2.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/summary2.xml new file mode 100644 index 000000000..49aa117aa --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/summary2.xml @@ -0,0 +1,966 @@ + + + https://orcid.org/0000-0001-6816-8350 + 0000-0001-6816-8350 + orcid.org + + + en + + + Direct + 2016-01-06T05:08:45.720Z + 2024-01-02T20:07:05.186Z + true + true + true + + + 2023-12-02T13:32:05.269Z + + + 2016-02-09T09:18:18.417Z + + 2016-02-09T09:18:18.416Z + 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