From 1a42a5c10d401b932e81a9e3ebedbb9e875592f6 Mon Sep 17 00:00:00 2001 From: "sandro.labruzzo" Date: Wed, 10 Jan 2024 18:03:20 +0100 Subject: [PATCH 01/10] Implemented Download update of ORCID --- .../dhp/collection/orcid/ORCIDWorker.java | 236 ++++++++++++++++++ .../collection/orcid/OrcidGetUpdatesFile.java | 133 ++++++++++ .../download_orcid_update_parameter.json | 27 ++ .../collection/orcid/DownloadORCIDTest.java | 21 ++ .../provision/IndexRecordTransformerTest.java | 2 +- 5 files changed, 418 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java new file mode 100644 index 000000000..9560c36a2 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java @@ -0,0 +1,236 @@ +package eu.dnetlib.dhp.collection.orcid; + +import eu.dnetlib.dhp.common.collection.HttpClientParams; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.apache.http.HttpHeaders; +import org.jetbrains.annotations.NotNull; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import javax.swing.*; +import java.io.IOException; +import java.io.InputStream; +import java.net.HttpURLConnection; +import java.net.URL; +import java.util.concurrent.BlockingQueue; + +public class ORCIDWorker extends Thread { + + final static Logger log = LoggerFactory.getLogger(ORCIDWorker.class); + + public static String JOB_COMPLETE="JOB_COMPLETE"; + + private static final String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)"; + + private final BlockingQueue queue; + + private boolean hasComplete = false; + + private final SequenceFile.Writer employments; + + private final SequenceFile.Writer summary; + private final SequenceFile.Writer works; + + private final String token; + + private final String id; + + public static ORCIDWorkerBuilder builder() { + return new ORCIDWorkerBuilder(); + } + + public ORCIDWorker(String id, BlockingQueue myqueue, SequenceFile.Writer employments, SequenceFile.Writer summary, SequenceFile.Writer works, String token) { + this.id= id; + this.queue = myqueue; + this.employments = employments; + this.summary = summary; + this.works = works; + this.token = token; + } + + + public static String retrieveURL(final String id,final String apiUrl, String token) { + try { + final HttpURLConnection urlConn = getHttpURLConnection(apiUrl, token); + if (urlConn.getResponseCode()>199 && urlConn.getResponseCode()<300) { + InputStream input = urlConn.getInputStream(); + return IOUtils.toString(input); + } else { + log.error("Thread {} UNABLE TO DOWNLOAD FROM THIS URL {} , status code {}",id, apiUrl,urlConn.getResponseCode()); + } + } catch (Exception e) { + log.error("Thread {} Error on retrieving URL {} {}",id,apiUrl, e); + } + return null; + } + + @NotNull + private static HttpURLConnection getHttpURLConnection(String apiUrl, String token) throws IOException { + final HttpURLConnection urlConn = (HttpURLConnection) new URL(apiUrl).openConnection(); + final HttpClientParams clientParams = new HttpClientParams(); + urlConn.setInstanceFollowRedirects(false); + urlConn.setReadTimeout(clientParams.getReadTimeOut() * 1000); + urlConn.setConnectTimeout(clientParams.getConnectTimeOut() * 1000); + urlConn.addRequestProperty(HttpHeaders.USER_AGENT, userAgent); + urlConn.addRequestProperty(HttpHeaders.AUTHORIZATION, String.format("Bearer %s", token)); + return urlConn; + } + + private static String generateSummaryURL(final String orcidId) { + return "https://api.orcid.org/v3.0/" + orcidId + "/record"; + } + + private static String generateWorksURL(final String orcidId) { + return "https://api.orcid.org/v3.0/" + orcidId + "/works"; + } + private static String generateEmploymentsURL(final String orcidId) { + return "https://api.orcid.org/v3.0/" + orcidId + "/employments"; + } + + + private static void writeResultToSequenceFile(String id, String url, String token, String orcidId, SequenceFile.Writer file) throws IOException { + final String response = retrieveURL(id, url,token); + if (response!= null) { + + if(orcidId==null || response ==null){ + log.error("Thread {} {} {}",id, orcidId, response); + throw new RuntimeException("null items "); + } + + if(file==null) { + log.error("Thread {} file is null for {} URL:{}",id, url, orcidId); + } + else + file.append(new Text(orcidId),new Text(response)); + } + + } + + + @Override + public void run() { + final Text key = new Text(); + final Text value = new Text(); + long start; + long total_time; + String orcidId=""; + int requests =0; + if(summary==null || employments==null || works == null) + throw new RuntimeException("Null files"); + + while (!hasComplete) { + try { + + orcidId = queue.take(); + + if (orcidId.equalsIgnoreCase(JOB_COMPLETE)) { + queue.put(orcidId); + hasComplete = true; + } else { + start = System.currentTimeMillis(); + writeResultToSequenceFile(id, generateSummaryURL(orcidId), token,orcidId, summary); + total_time = System.currentTimeMillis() - start; + requests++; + if (total_time < 1000) { + Thread.sleep(1000L - total_time); + } + start = System.currentTimeMillis(); + writeResultToSequenceFile(id, generateWorksURL(orcidId),token,orcidId, works); + total_time = System.currentTimeMillis() - start; + requests++; + if (total_time < 1000) { + Thread.sleep(1000L - total_time); + } + start = System.currentTimeMillis(); + writeResultToSequenceFile(id, generateEmploymentsURL(orcidId),token,orcidId, employments); + total_time = System.currentTimeMillis() - start; + requests++; + if (total_time < 1000) { + Thread.sleep(1000L - total_time); + } + if (requests %30 ==0) + { + log.info("Thread {} Downloaded {}",id, requests); + } + } + + + } catch (Throwable e) { + + log.error("Thread {} Unable to save ORICD: {} item error",id, orcidId,e); + + } + + } + try { + works.close(); + summary.close(); + employments.close(); + } catch (Throwable e) { + throw new RuntimeException(e); + } + + + log.info("Thread {} COMPLETE ", id); + log.info("Thread {} Downloaded {}", id, requests); + + } + + + public static class ORCIDWorkerBuilder { + + private String id; + private SequenceFile.Writer employments; + private SequenceFile.Writer summary; + private SequenceFile.Writer works; + private BlockingQueue queue; + + private String token; + + public ORCIDWorkerBuilder withId(final String id) { + this.id =id; + return this; + } + + public ORCIDWorkerBuilder withEmployments(final SequenceFile.Writer sequenceFile) { + this.employments = sequenceFile; + return this; + } + + + public ORCIDWorkerBuilder withSummary(final SequenceFile.Writer sequenceFile) { + this.summary = sequenceFile; + return this; + } + + public ORCIDWorkerBuilder withWorks(final SequenceFile.Writer sequenceFile) { + this.works = sequenceFile; + return this; + } + + public ORCIDWorkerBuilder withAccessToken(final String accessToken) { + this.token = accessToken; + return this; + } + + public ORCIDWorkerBuilder withBlockingQueue(final BlockingQueue queue) { + this.queue = queue; + return this; + } + + + public ORCIDWorker build() { + if (this.summary== null || this.works==null || this.employments == null || StringUtils.isEmpty(token) || queue == null) + throw new RuntimeException("Unable to build missing required params"); + return new ORCIDWorker(id, queue,employments,summary,works,token); + } + + + + } + + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java new file mode 100644 index 000000000..3bfe72328 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java @@ -0,0 +1,133 @@ + +package eu.dnetlib.dhp.collection.orcid; + +import java.io.*; +import java.net.HttpURLConnection; +import java.net.URL; +import java.util.ArrayList; +import java.util.List; +import java.util.concurrent.ArrayBlockingQueue; +import java.util.concurrent.BlockingQueue; + +import eu.dnetlib.dhp.common.collection.HttpClientParams; +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration; + +public class OrcidGetUpdatesFile { + + private static Logger log = LoggerFactory.getLogger(OrcidGetUpdatesFile.class); + + public static void main(String[] args) throws IOException { + + ArgumentApplicationParser parser = new ArgumentApplicationParser( + "/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json"); + + final String namenode = parser.get("namenode"); + log.info("got variable namenode: {}", namenode); + + final String targetPath = parser.get("targetPath"); + log.info("got variable targetPath: {}", targetPath); + + //http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar + final String apiURL = parser.get("apiURL"); + log.info("got variable apiURL: {}", apiURL); + + final String accessToken = parser.get("accessToken"); + log.info("got variable accessToken: {}", accessToken); + + + + final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(namenode)); + + + } + + private SequenceFile.Writer createFile(Path aPath, FileSystem fileSystem) throws IOException { + return SequenceFile + .createWriter( + fileSystem.getConf(), + SequenceFile.Writer.file(aPath), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class)); + } + + + private ORCIDWorker createWorker(final String id, final String targetPath, final BlockingQueue queue, final String accessToken, FileSystem fileSystem) throws Exception { + return ORCIDWorker.builder() + .withId(id) + .withEmployments(createFile(new Path(String.format("%s/employments_%s", targetPath, id)), fileSystem)) + .withSummary(createFile(new Path(String.format("%s/summary_%s", targetPath, id)), fileSystem)) + .withWorks(createFile(new Path(String.format("%s/works_%s", targetPath, id)), fileSystem)) + .withAccessToken(accessToken) + .withBlockingQueue(queue) + .build(); + } + + + + public void readTar(FileSystem fileSystem, final String accessToken, final String apiURL, final String targetPath, final String startDate ) throws Exception { + final HttpURLConnection urlConn = (HttpURLConnection) new URL(apiURL).openConnection(); + final HttpClientParams clientParams = new HttpClientParams(); + urlConn.setInstanceFollowRedirects(false); + urlConn.setReadTimeout(clientParams.getReadTimeOut() * 1000); + urlConn.setConnectTimeout(clientParams.getConnectTimeOut() * 1000); + if (urlConn.getResponseCode()>199 && urlConn.getResponseCode()<300) { + InputStream input = urlConn.getInputStream(); + TarArchiveInputStream tais = new TarArchiveInputStream(new GzipCompressorInputStream( + new BufferedInputStream( + input))); + TarArchiveEntry entry; + + BlockingQueue queue = new ArrayBlockingQueue(3000); + final List workers = new ArrayList<>(); + for (int i = 0; i <20; i++) { + workers.add(createWorker(""+i,targetPath,queue,accessToken, fileSystem)); + } + workers.forEach(Thread::start); + + + while ((entry = tais.getNextTarEntry()) != null) { + + if (entry.isFile()) { + + BufferedReader br = new BufferedReader(new InputStreamReader(tais)); + System.out.println(br.readLine()); + br.lines().map(l -> l.split(",")).filter(s -> StringUtils.compare(s[3].substring(0, 10), startDate) > 0).map(s->s[0]).limit(200).forEach(s -> { + try { + log.info("Adding item "); + queue.put(s); + } catch (InterruptedException e) { + throw new RuntimeException(e); + } + }); + queue.put(ORCIDWorker.JOB_COMPLETE); + + } + } + + for (ORCIDWorker worker : workers) { + worker.join(); + } + + + } + + + + + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json new file mode 100644 index 000000000..dbadf86cb --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json @@ -0,0 +1,27 @@ +[ + { + "paramName": "n", + "paramLongName": "namenode", + "paramDescription": "the Name Node URI", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target PATH where download the files", + "paramRequired": true + }, + { + "paramName": "a", + "paramLongName": "apiURL", + "paramDescription": "the URL to download the tar file", + "paramRequired": true + }, + { + "paramName": "at", + "paramLongName": "accessToken", + "paramDescription": "the accessToken to contact API", + "paramRequired": true + } + +] \ No newline at end of file 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 868f4e92d..dc0393dc5 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 @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.collection.orcid; import java.io.IOException; +import java.net.URI; import java.util.Arrays; import java.util.List; import java.util.Objects; @@ -9,7 +10,12 @@ import java.util.Objects; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocalFileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.apache.spark.SparkContext; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.sql.Encoders; @@ -116,4 +122,19 @@ public class DownloadORCIDTest { }); } +// @Test +// public void testReadTar() throws Exception { +//// new OrcidGetUpdatesFile().readTar(); +// +// Configuration conf = new Configuration(); +// FileSystem fs = FileSystem.get(URI.create("file:///"), conf); +// final String token ="78fdb232-7105-4086-8570-e153f4198e3d"; +// +// new OrcidGetUpdatesFile().readTar(fs,token, "http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar", "file:///Users/sandro/orcid","2023-09-30"); +// +// +// +// +// } + } diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java index e07ba1b4e..e72883055 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java @@ -82,7 +82,7 @@ public class IndexRecordTransformerTest { void testPeerReviewed() throws IOException, TransformerException { final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, - XmlConverterJob.schemaLocation); + XmlConverterJob.schemaLocation); final Publication p = load("publication.json", Publication.class); -- 2.17.1 From 8f61063201720534116a092b375131415ac149e7 Mon Sep 17 00:00:00 2001 From: "sandro.labruzzo" Date: Wed, 10 Jan 2024 19:42:22 +0100 Subject: [PATCH 02/10] Added workflow --- .../collection/orcid/OrcidGetUpdatesFile.java | 2 +- .../orcid/update/oozie_app/config-default.xml | 23 +++++++ .../orcid/update/oozie_app/workflow.xml | 69 +++++++++++++++++++ 3 files changed, 93 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java index 3bfe72328..39da749e2 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java @@ -41,7 +41,7 @@ public class OrcidGetUpdatesFile { final String targetPath = parser.get("targetPath"); log.info("got variable targetPath: {}", targetPath); - //http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar + final String apiURL = parser.get("apiURL"); log.info("got variable apiURL: {}", apiURL); diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/config-default.xml new file mode 100644 index 000000000..dd3c32c62 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/config-default.xml @@ -0,0 +1,23 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ 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 new file mode 100644 index 000000000..74a88bae6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/workflow.xml @@ -0,0 +1,69 @@ + + + + targetPath + the path to store the original ORCID dump + + + apiURL + The URL of the update CSV list + http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar + + + accessToken + The access tocken + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.collection.orcid.OrcidGetUpdatesFile + --namenode${nameNode} + --targetPath${targetPath} + --apiURL${apiURL} + --accessToken${accessToken} + + + + + + + + yarn + cluster + Generate ORCID Tables + eu.dnetlib.dhp.collection.orcid.SparkGenerateORCIDTable + dhp-aggregation-${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} + + --sourcePath${targetPath}/extracted + --targetPath${targetPath}/tables + --masteryarn + + + + + + \ No newline at end of file -- 2.17.1 From 9d5a7c3b2254d90ccaa7ac85a89c063d9a0ea5c8 Mon Sep 17 00:00:00 2001 From: "sandro.labruzzo" Date: Wed, 10 Jan 2024 19:42:34 +0100 Subject: [PATCH 03/10] code refactor --- .../dhp/oa/provision/XmlIndexingJobTest.java | 29 +++++++++---------- 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java index b62acbac3..a3a140cf6 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java @@ -1,6 +1,8 @@ package eu.dnetlib.dhp.oa.provision; +import static org.junit.jupiter.api.Assertions.assertEquals; + import java.io.IOException; import java.io.StringReader; import java.net.URI; @@ -32,8 +34,6 @@ import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import static org.junit.jupiter.api.Assertions.assertEquals; - @ExtendWith(MockitoExtension.class) public class XmlIndexingJobTest extends SolrTest { @@ -110,34 +110,33 @@ public class XmlIndexingJobTest extends SolrTest { QueryResponse rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "*:*")); assertEquals( - nRecord, rsp.getResults().getNumFound(), - "the number of indexed records should be equal to the number of input records"); - + nRecord, rsp.getResults().getNumFound(), + "the number of indexed records should be equal to the number of input records"); rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "isgreen:true")); assertEquals( - 0, rsp.getResults().getNumFound(), - "the number of indexed records having isgreen = true"); + 0, rsp.getResults().getNumFound(), + "the number of indexed records having isgreen = true"); rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "openaccesscolor:bronze")); assertEquals( - 0, rsp.getResults().getNumFound(), - "the number of indexed records having openaccesscolor = bronze"); + 0, rsp.getResults().getNumFound(), + "the number of indexed records having openaccesscolor = bronze"); rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "isindiamondjournal:true")); assertEquals( - 0, rsp.getResults().getNumFound(), - "the number of indexed records having isindiamondjournal = true"); + 0, rsp.getResults().getNumFound(), + "the number of indexed records having isindiamondjournal = true"); rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "publiclyfunded:true")); assertEquals( - 0, rsp.getResults().getNumFound(), - "the number of indexed records having publiclyfunded = true"); + 0, rsp.getResults().getNumFound(), + "the number of indexed records having publiclyfunded = true"); rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "peerreviewed:true")); assertEquals( - 0, rsp.getResults().getNumFound(), - "the number of indexed records having peerreviewed = true"); + 0, rsp.getResults().getNumFound(), + "the number of indexed records having peerreviewed = true"); } @Test -- 2.17.1 From 859babf7223990d0f5146fb6dc45dd73a251127a Mon Sep 17 00:00:00 2001 From: "sandro.labruzzo" Date: Wed, 10 Jan 2024 19:51:13 +0100 Subject: [PATCH 04/10] added some useful comment --- .../java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java index 9560c36a2..0abebd8b8 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java @@ -135,6 +135,8 @@ public class ORCIDWorker extends Thread { total_time = System.currentTimeMillis() - start; requests++; if (total_time < 1000) { + //I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds, hence + //the time between two http request in a thread must be 1 second Thread.sleep(1000L - total_time); } start = System.currentTimeMillis(); @@ -142,6 +144,8 @@ public class ORCIDWorker extends Thread { total_time = System.currentTimeMillis() - start; requests++; if (total_time < 1000) { + //I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds, hence + //the time between two http request in a thread must be 1 second Thread.sleep(1000L - total_time); } start = System.currentTimeMillis(); @@ -149,6 +153,8 @@ public class ORCIDWorker extends Thread { total_time = System.currentTimeMillis() - start; requests++; if (total_time < 1000) { + //I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds, hence + //the time between two http request in a thread must be 1 second Thread.sleep(1000L - total_time); } if (requests %30 ==0) -- 2.17.1 From e328bc0adea9befeb00005f08ffe78fcc20da6fc Mon Sep 17 00:00:00 2001 From: "sandro.labruzzo" <@lice29> Date: Fri, 12 Jan 2024 16:18:20 +0100 Subject: [PATCH 05/10] fixed missing parameter on download update --- .../dhp/collection/orcid/ORCIDWorker.java | 372 +++++++++--------- .../collection/orcid/OrcidGetUpdatesFile.java | 125 +++--- .../download_orcid_update_parameter.json | 4 +- .../orcid/update/oozie_app/workflow.xml | 4 +- .../collection/orcid/DownloadORCIDTest.java | 13 +- 5 files changed, 259 insertions(+), 259 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java index 0abebd8b8..544262043 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java @@ -1,6 +1,14 @@ + package eu.dnetlib.dhp.collection.orcid; -import eu.dnetlib.dhp.common.collection.HttpClientParams; +import java.io.IOException; +import java.io.InputStream; +import java.net.HttpURLConnection; +import java.net.URL; +import java.util.concurrent.BlockingQueue; + +import javax.swing.*; + import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.io.SequenceFile; @@ -10,233 +18,225 @@ import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import javax.swing.*; -import java.io.IOException; -import java.io.InputStream; -import java.net.HttpURLConnection; -import java.net.URL; -import java.util.concurrent.BlockingQueue; +import eu.dnetlib.dhp.common.collection.HttpClientParams; public class ORCIDWorker extends Thread { - final static Logger log = LoggerFactory.getLogger(ORCIDWorker.class); + final static Logger log = LoggerFactory.getLogger(ORCIDWorker.class); - public static String JOB_COMPLETE="JOB_COMPLETE"; + public static String JOB_COMPLETE = "JOB_COMPLETE"; - private static final String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)"; + private static final String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)"; - private final BlockingQueue queue; + private final BlockingQueue queue; - private boolean hasComplete = false; + private boolean hasComplete = false; - private final SequenceFile.Writer employments; + private final SequenceFile.Writer employments; - private final SequenceFile.Writer summary; - private final SequenceFile.Writer works; + private final SequenceFile.Writer summary; + private final SequenceFile.Writer works; - private final String token; + private final String token; - private final String id; + private final String id; - public static ORCIDWorkerBuilder builder() { - return new ORCIDWorkerBuilder(); - } + public static ORCIDWorkerBuilder builder() { + return new ORCIDWorkerBuilder(); + } - public ORCIDWorker(String id, BlockingQueue myqueue, SequenceFile.Writer employments, SequenceFile.Writer summary, SequenceFile.Writer works, String token) { - this.id= id; - this.queue = myqueue; - this.employments = employments; - this.summary = summary; - this.works = works; - this.token = token; - } + public ORCIDWorker(String id, BlockingQueue myqueue, SequenceFile.Writer employments, + SequenceFile.Writer summary, SequenceFile.Writer works, String token) { + this.id = id; + this.queue = myqueue; + this.employments = employments; + this.summary = summary; + this.works = works; + this.token = token; + } + public static String retrieveURL(final String id, final String apiUrl, String token) { + try { + final HttpURLConnection urlConn = getHttpURLConnection(apiUrl, token); + if (urlConn.getResponseCode() > 199 && urlConn.getResponseCode() < 300) { + InputStream input = urlConn.getInputStream(); + return IOUtils.toString(input); + } else { + log + .error( + "Thread {} UNABLE TO DOWNLOAD FROM THIS URL {} , status code {}", id, apiUrl, + urlConn.getResponseCode()); + } + } catch (Exception e) { + log.error("Thread {} Error on retrieving URL {} {}", id, apiUrl, e); + } + return null; + } - public static String retrieveURL(final String id,final String apiUrl, String token) { - try { - final HttpURLConnection urlConn = getHttpURLConnection(apiUrl, token); - if (urlConn.getResponseCode()>199 && urlConn.getResponseCode()<300) { - InputStream input = urlConn.getInputStream(); - return IOUtils.toString(input); - } else { - log.error("Thread {} UNABLE TO DOWNLOAD FROM THIS URL {} , status code {}",id, apiUrl,urlConn.getResponseCode()); - } - } catch (Exception e) { - log.error("Thread {} Error on retrieving URL {} {}",id,apiUrl, e); - } - return null; - } + @NotNull + private static HttpURLConnection getHttpURLConnection(String apiUrl, String token) throws IOException { + final HttpURLConnection urlConn = (HttpURLConnection) new URL(apiUrl).openConnection(); + final HttpClientParams clientParams = new HttpClientParams(); + urlConn.setInstanceFollowRedirects(false); + urlConn.setReadTimeout(clientParams.getReadTimeOut() * 1000); + urlConn.setConnectTimeout(clientParams.getConnectTimeOut() * 1000); + urlConn.addRequestProperty(HttpHeaders.USER_AGENT, userAgent); + urlConn.addRequestProperty(HttpHeaders.AUTHORIZATION, String.format("Bearer %s", token)); + return urlConn; + } - @NotNull - private static HttpURLConnection getHttpURLConnection(String apiUrl, String token) throws IOException { - final HttpURLConnection urlConn = (HttpURLConnection) new URL(apiUrl).openConnection(); - final HttpClientParams clientParams = new HttpClientParams(); - urlConn.setInstanceFollowRedirects(false); - urlConn.setReadTimeout(clientParams.getReadTimeOut() * 1000); - urlConn.setConnectTimeout(clientParams.getConnectTimeOut() * 1000); - urlConn.addRequestProperty(HttpHeaders.USER_AGENT, userAgent); - urlConn.addRequestProperty(HttpHeaders.AUTHORIZATION, String.format("Bearer %s", token)); - return urlConn; - } + private static String generateSummaryURL(final String orcidId) { + return "https://api.orcid.org/v3.0/" + orcidId + "/record"; + } - private static String generateSummaryURL(final String orcidId) { - return "https://api.orcid.org/v3.0/" + orcidId + "/record"; - } + private static String generateWorksURL(final String orcidId) { + return "https://api.orcid.org/v3.0/" + orcidId + "/works"; + } - private static String generateWorksURL(final String orcidId) { - return "https://api.orcid.org/v3.0/" + orcidId + "/works"; - } - private static String generateEmploymentsURL(final String orcidId) { - return "https://api.orcid.org/v3.0/" + orcidId + "/employments"; - } + private static String generateEmploymentsURL(final String orcidId) { + return "https://api.orcid.org/v3.0/" + orcidId + "/employments"; + } + private static void writeResultToSequenceFile(String id, String url, String token, String orcidId, + SequenceFile.Writer file) throws IOException { + final String response = retrieveURL(id, url, token); + if (response != null) { - private static void writeResultToSequenceFile(String id, String url, String token, String orcidId, SequenceFile.Writer file) throws IOException { - final String response = retrieveURL(id, url,token); - if (response!= null) { + if (orcidId == null || response == null) { + log.error("Thread {} {} {}", id, orcidId, response); + throw new RuntimeException("null items "); + } - if(orcidId==null || response ==null){ - log.error("Thread {} {} {}",id, orcidId, response); - throw new RuntimeException("null items "); - } + if (file == null) { + log.error("Thread {} file is null for {} URL:{}", id, url, orcidId); + } else + file.append(new Text(orcidId), new Text(response)); + } - if(file==null) { - log.error("Thread {} file is null for {} URL:{}",id, url, orcidId); - } - else - file.append(new Text(orcidId),new Text(response)); - } + } - } + @Override + public void run() { + final Text key = new Text(); + final Text value = new Text(); + long start; + long total_time; + String orcidId = ""; + int requests = 0; + if (summary == null || employments == null || works == null) + throw new RuntimeException("Null files"); + while (!hasComplete) { + try { - @Override - public void run() { - final Text key = new Text(); - final Text value = new Text(); - long start; - long total_time; - String orcidId=""; - int requests =0; - if(summary==null || employments==null || works == null) - throw new RuntimeException("Null files"); + orcidId = queue.take(); - while (!hasComplete) { - try { + if (orcidId.equalsIgnoreCase(JOB_COMPLETE)) { + queue.put(orcidId); + hasComplete = true; + } else { + start = System.currentTimeMillis(); + writeResultToSequenceFile(id, generateSummaryURL(orcidId), token, orcidId, summary); + total_time = System.currentTimeMillis() - start; + requests++; + if (total_time < 1000) { + // I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds, + // hence + // the time between two http request in a thread must be 1 second + Thread.sleep(1000L - total_time); + } + start = System.currentTimeMillis(); + writeResultToSequenceFile(id, generateWorksURL(orcidId), token, orcidId, works); + total_time = System.currentTimeMillis() - start; + requests++; + if (total_time < 1000) { + // I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds, + // hence + // the time between two http request in a thread must be 1 second + Thread.sleep(1000L - total_time); + } + start = System.currentTimeMillis(); + writeResultToSequenceFile(id, generateEmploymentsURL(orcidId), token, orcidId, employments); + total_time = System.currentTimeMillis() - start; + requests++; + if (total_time < 1000) { + // I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds, + // hence + // the time between two http request in a thread must be 1 second + Thread.sleep(1000L - total_time); + } + if (requests % 30 == 0) { + log.info("Thread {} Downloaded {}", id, requests); + } + } - orcidId = queue.take(); + } catch (Throwable e) { - if (orcidId.equalsIgnoreCase(JOB_COMPLETE)) { - queue.put(orcidId); - hasComplete = true; - } else { - start = System.currentTimeMillis(); - writeResultToSequenceFile(id, generateSummaryURL(orcidId), token,orcidId, summary); - total_time = System.currentTimeMillis() - start; - requests++; - if (total_time < 1000) { - //I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds, hence - //the time between two http request in a thread must be 1 second - Thread.sleep(1000L - total_time); - } - start = System.currentTimeMillis(); - writeResultToSequenceFile(id, generateWorksURL(orcidId),token,orcidId, works); - total_time = System.currentTimeMillis() - start; - requests++; - if (total_time < 1000) { - //I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds, hence - //the time between two http request in a thread must be 1 second - Thread.sleep(1000L - total_time); - } - start = System.currentTimeMillis(); - writeResultToSequenceFile(id, generateEmploymentsURL(orcidId),token,orcidId, employments); - total_time = System.currentTimeMillis() - start; - requests++; - if (total_time < 1000) { - //I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds, hence - //the time between two http request in a thread must be 1 second - Thread.sleep(1000L - total_time); - } - if (requests %30 ==0) - { - log.info("Thread {} Downloaded {}",id, requests); - } - } + log.error("Thread {} Unable to save ORICD: {} item error", id, orcidId, e); + } - } catch (Throwable e) { + } + try { + works.close(); + summary.close(); + employments.close(); + } catch (Throwable e) { + throw new RuntimeException(e); + } - log.error("Thread {} Unable to save ORICD: {} item error",id, orcidId,e); + log.info("Thread {} COMPLETE ", id); + log.info("Thread {} Downloaded {}", id, requests); - } + } - } - try { - works.close(); - summary.close(); - employments.close(); - } catch (Throwable e) { - throw new RuntimeException(e); - } + public static class ORCIDWorkerBuilder { + private String id; + private SequenceFile.Writer employments; + private SequenceFile.Writer summary; + private SequenceFile.Writer works; + private BlockingQueue queue; - log.info("Thread {} COMPLETE ", id); - log.info("Thread {} Downloaded {}", id, requests); + private String token; - } + public ORCIDWorkerBuilder withId(final String id) { + this.id = id; + return this; + } + public ORCIDWorkerBuilder withEmployments(final SequenceFile.Writer sequenceFile) { + this.employments = sequenceFile; + return this; + } - public static class ORCIDWorkerBuilder { + public ORCIDWorkerBuilder withSummary(final SequenceFile.Writer sequenceFile) { + this.summary = sequenceFile; + return this; + } - private String id; - private SequenceFile.Writer employments; - private SequenceFile.Writer summary; - private SequenceFile.Writer works; - private BlockingQueue queue; + public ORCIDWorkerBuilder withWorks(final SequenceFile.Writer sequenceFile) { + this.works = sequenceFile; + return this; + } - private String token; + public ORCIDWorkerBuilder withAccessToken(final String accessToken) { + this.token = accessToken; + return this; + } - public ORCIDWorkerBuilder withId(final String id) { - this.id =id; - return this; - } + public ORCIDWorkerBuilder withBlockingQueue(final BlockingQueue queue) { + this.queue = queue; + return this; + } - public ORCIDWorkerBuilder withEmployments(final SequenceFile.Writer sequenceFile) { - this.employments = sequenceFile; - return this; - } - - - public ORCIDWorkerBuilder withSummary(final SequenceFile.Writer sequenceFile) { - this.summary = sequenceFile; - return this; - } - - public ORCIDWorkerBuilder withWorks(final SequenceFile.Writer sequenceFile) { - this.works = sequenceFile; - return this; - } - - public ORCIDWorkerBuilder withAccessToken(final String accessToken) { - this.token = accessToken; - return this; - } - - public ORCIDWorkerBuilder withBlockingQueue(final BlockingQueue queue) { - this.queue = queue; - return this; - } - - - public ORCIDWorker build() { - if (this.summary== null || this.works==null || this.employments == null || StringUtils.isEmpty(token) || queue == null) - throw new RuntimeException("Unable to build missing required params"); - return new ORCIDWorker(id, queue,employments,summary,works,token); - } - - - - } + public ORCIDWorker build() { + if (this.summary == null || this.works == null || this.employments == null || StringUtils.isEmpty(token) + || queue == null) + throw new RuntimeException("Unable to build missing required params"); + return new ORCIDWorker(id, queue, employments, summary, works, token); + } + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java index 39da749e2..6438d737c 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java @@ -1,15 +1,17 @@ package eu.dnetlib.dhp.collection.orcid; +import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration; + import java.io.*; import java.net.HttpURLConnection; import java.net.URL; import java.util.ArrayList; import java.util.List; +import java.util.Objects; import java.util.concurrent.ArrayBlockingQueue; import java.util.concurrent.BlockingQueue; -import eu.dnetlib.dhp.common.collection.HttpClientParams; import org.apache.commons.compress.archivers.tar.TarArchiveEntry; import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream; @@ -23,96 +25,108 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; - -import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration; +import eu.dnetlib.dhp.common.collection.HttpClientParams; public class OrcidGetUpdatesFile { - private static Logger log = LoggerFactory.getLogger(OrcidGetUpdatesFile.class); + private static Logger log = LoggerFactory.getLogger(OrcidGetUpdatesFile.class); - public static void main(String[] args) throws IOException { + public static void main(String[] args) throws Exception { - ArgumentApplicationParser parser = new ArgumentApplicationParser( - "/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json"); + ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + Objects + .requireNonNull( + OrcidGetUpdatesFile.class + .getResourceAsStream( + "/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json"))) - final String namenode = parser.get("namenode"); - log.info("got variable namenode: {}", namenode); + ); + parser.parseArgument(args); - final String targetPath = parser.get("targetPath"); - log.info("got variable targetPath: {}", targetPath); + final String namenode = parser.get("namenode"); + log.info("got variable namenode: {}", namenode); + final String targetPath = parser.get("targetPath"); + log.info("got variable targetPath: {}", targetPath); - final String apiURL = parser.get("apiURL"); - log.info("got variable apiURL: {}", apiURL); + final String apiURL = parser.get("apiURL"); + log.info("got variable apiURL: {}", apiURL); final String accessToken = parser.get("accessToken"); log.info("got variable accessToken: {}", accessToken); + System.out.println("namenode = " + namenode); + final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(namenode)); - final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(namenode)); + new OrcidGetUpdatesFile().readTar(fileSystem, accessToken, apiURL, targetPath, "2023-09-30"); - - } - - private SequenceFile.Writer createFile(Path aPath, FileSystem fileSystem) throws IOException { - return SequenceFile - .createWriter( - fileSystem.getConf(), - SequenceFile.Writer.file(aPath), - SequenceFile.Writer.keyClass(Text.class), - SequenceFile.Writer.valueClass(Text.class)); } + private SequenceFile.Writer createFile(Path aPath, FileSystem fileSystem) throws IOException { + return SequenceFile + .createWriter( + fileSystem.getConf(), + SequenceFile.Writer.file(aPath), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class)); + } - private ORCIDWorker createWorker(final String id, final String targetPath, final BlockingQueue queue, final String accessToken, FileSystem fileSystem) throws Exception { - return ORCIDWorker.builder() - .withId(id) - .withEmployments(createFile(new Path(String.format("%s/employments_%s", targetPath, id)), fileSystem)) - .withSummary(createFile(new Path(String.format("%s/summary_%s", targetPath, id)), fileSystem)) - .withWorks(createFile(new Path(String.format("%s/works_%s", targetPath, id)), fileSystem)) - .withAccessToken(accessToken) - .withBlockingQueue(queue) - .build(); - } + private ORCIDWorker createWorker(final String id, final String targetPath, final BlockingQueue queue, + final String accessToken, FileSystem fileSystem) throws Exception { + return ORCIDWorker + .builder() + .withId(id) + .withEmployments(createFile(new Path(String.format("%s/employments_%s", targetPath, id)), fileSystem)) + .withSummary(createFile(new Path(String.format("%s/summary_%s", targetPath, id)), fileSystem)) + .withWorks(createFile(new Path(String.format("%s/works_%s", targetPath, id)), fileSystem)) + .withAccessToken(accessToken) + .withBlockingQueue(queue) + .build(); + } - - - public void readTar(FileSystem fileSystem, final String accessToken, final String apiURL, final String targetPath, final String startDate ) throws Exception { + public void readTar(FileSystem fileSystem, final String accessToken, final String apiURL, final String targetPath, + final String startDate) throws Exception { final HttpURLConnection urlConn = (HttpURLConnection) new URL(apiURL).openConnection(); final HttpClientParams clientParams = new HttpClientParams(); urlConn.setInstanceFollowRedirects(false); urlConn.setReadTimeout(clientParams.getReadTimeOut() * 1000); urlConn.setConnectTimeout(clientParams.getConnectTimeOut() * 1000); - if (urlConn.getResponseCode()>199 && urlConn.getResponseCode()<300) { + if (urlConn.getResponseCode() > 199 && urlConn.getResponseCode() < 300) { InputStream input = urlConn.getInputStream(); TarArchiveInputStream tais = new TarArchiveInputStream(new GzipCompressorInputStream( - new BufferedInputStream( - input))); + new BufferedInputStream( + input))); TarArchiveEntry entry; BlockingQueue queue = new ArrayBlockingQueue(3000); final List workers = new ArrayList<>(); - for (int i = 0; i <20; i++) { - workers.add(createWorker(""+i,targetPath,queue,accessToken, fileSystem)); + for (int i = 0; i < 22; i++) { + workers.add(createWorker("" + i, targetPath, queue, accessToken, fileSystem)); } workers.forEach(Thread::start); - - while ((entry = tais.getNextTarEntry()) != null) { + while ((entry = tais.getNextTarEntry()) != null) { if (entry.isFile()) { BufferedReader br = new BufferedReader(new InputStreamReader(tais)); System.out.println(br.readLine()); - br.lines().map(l -> l.split(",")).filter(s -> StringUtils.compare(s[3].substring(0, 10), startDate) > 0).map(s->s[0]).limit(200).forEach(s -> { - try { - log.info("Adding item "); - queue.put(s); - } catch (InterruptedException e) { - throw new RuntimeException(e); - } - }); + br + .lines() + .map(l -> l.split(",")) + .filter(s -> StringUtils.compare(s[3].substring(0, 10), startDate) > 0) + .map(s -> s[0]) + .forEach(s -> { + try { + log.info("Adding item "); + queue.put(s); + } catch (InterruptedException e) { + throw new RuntimeException(e); + } + }); queue.put(ORCIDWorker.JOB_COMPLETE); } @@ -122,12 +136,7 @@ public class OrcidGetUpdatesFile { worker.join(); } - } - - - - - } + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json index dbadf86cb..dbf63a31a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json @@ -1,5 +1,4 @@ -[ - { +[ { "paramName": "n", "paramLongName": "namenode", "paramDescription": "the Name Node URI", @@ -23,5 +22,4 @@ "paramDescription": "the accessToken to contact API", "paramRequired": true } - ] \ 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 74a88bae6..d7a81b022 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 @@ -6,12 +6,12 @@ apiURL - The URL of the update CSV list http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar + The URL of the update CSV list accessToken - The access tocken + The access token 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 dc0393dc5..846282721 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 @@ -124,16 +124,9 @@ public class DownloadORCIDTest { // @Test // public void testReadTar() throws Exception { -//// new OrcidGetUpdatesFile().readTar(); -// -// Configuration conf = new Configuration(); -// FileSystem fs = FileSystem.get(URI.create("file:///"), conf); -// final String token ="78fdb232-7105-4086-8570-e153f4198e3d"; -// -// new OrcidGetUpdatesFile().readTar(fs,token, "http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar", "file:///Users/sandro/orcid","2023-09-30"); -// -// -// +// OrcidGetUpdatesFile.main(new String[] { +// "--namenode", "puppa" +// }); // // } -- 2.17.1 From e0753f19da7a33978d57016a6781076458a09186 Mon Sep 17 00:00:00 2001 From: "sandro.labruzzo" Date: Sat, 13 Jan 2024 09:27:08 +0100 Subject: [PATCH 06/10] Fixed error of connection timeout --- .../eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java | 8 +++++--- .../dhp/collection/orcid/OrcidGetUpdatesFile.java | 9 ++++++++- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java index 544262043..db6475dfa 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java @@ -101,16 +101,18 @@ public class ORCIDWorker extends Thread { SequenceFile.Writer file) throws IOException { final String response = retrieveURL(id, url, token); if (response != null) { - - if (orcidId == null || response == null) { + if (orcidId == null) { log.error("Thread {} {} {}", id, orcidId, response); throw new RuntimeException("null items "); } if (file == null) { log.error("Thread {} file is null for {} URL:{}", id, url, orcidId); - } else + } else { file.append(new Text(orcidId), new Text(response)); + file.hflush(); + } + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java index 6438d737c..388d32b4e 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java @@ -17,6 +17,8 @@ import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.fs.FSDataInputStream; +import org.apache.hadoop.fs.FSDataOutputStream; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.SequenceFile; @@ -96,9 +98,14 @@ public class OrcidGetUpdatesFile { urlConn.setConnectTimeout(clientParams.getConnectTimeOut() * 1000); if (urlConn.getResponseCode() > 199 && urlConn.getResponseCode() < 300) { InputStream input = urlConn.getInputStream(); + + Path hdfsWritePath = new Path("/tmp/orcid_updates.tar.gz"); + final FSDataOutputStream fsDataOutputStream = fileSystem.create(hdfsWritePath, true); + IOUtils.copy(input, fsDataOutputStream); + FSDataInputStream updateFile = fileSystem.open(hdfsWritePath); TarArchiveInputStream tais = new TarArchiveInputStream(new GzipCompressorInputStream( new BufferedInputStream( - input))); + updateFile.getWrappedStream()))); TarArchiveEntry entry; BlockingQueue queue = new ArrayBlockingQueue(3000); -- 2.17.1 From 43e0bba7eda73b825a3192c7f9794e2f125fe272 Mon Sep 17 00:00:00 2001 From: "sandro.labruzzo" Date: Tue, 23 Jan 2024 15:04:49 +0100 Subject: [PATCH 07/10] logg added during download --- .../main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java | 3 ++- .../eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java | 1 - 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java index db6475dfa..fe59fe71f 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java @@ -113,7 +113,8 @@ public class ORCIDWorker extends Thread { file.hflush(); } - } + } else + log.error("Thread {} response is null for {} URL:{}", id, url, orcidId); } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java index 388d32b4e..2ba131e0f 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java @@ -128,7 +128,6 @@ public class OrcidGetUpdatesFile { .map(s -> s[0]) .forEach(s -> { try { - log.info("Adding item "); queue.put(s); } catch (InterruptedException e) { throw new RuntimeException(e); -- 2.17.1 From 0386f3638592766ac5b8972afcd23292d5c372a5 Mon Sep 17 00:00:00 2001 From: "sandro.labruzzo" Date: Thu, 25 Jan 2024 19:40:59 +0100 Subject: [PATCH 08/10] 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 + 2016-02-09T09:18:18.417Z + + + https://orcid.org/0000-0001-6816-8350 + 0000-0001-6816-8350 + orcid.org + + + Dr Michael Muchiri + http://www.rmit.edu.au/contact/staff-contacts/academic-staff/m/muchiri-dr-michael + + + + + 2023-12-02T13:32:05.269Z + + 2018-02-13T02:32:04.094Z + 2023-12-02T13:32:05.269Z + + + https://orcid.org/0000-0001-6816-8350 + 0000-0001-6816-8350 + orcid.org + + + AU + + + 2023-12-02T13:32:05.260Z + 2023-12-02T13:32:05.260Z + + + https://orcid.org/0000-0001-6816-8350 + 0000-0001-6816-8350 + orcid.org + + + SA + + + + 2023-12-02T13:31:16.269Z + + 2016-02-09T09:16:44.001Z + 2023-12-02T13:31:16.269Z + + + https://orcid.org/0000-0001-6816-8350 + 0000-0001-6816-8350 + orcid.org + + + Organizational Behavior + + + 2016-02-09T09:16:27.374Z + 2023-12-02T13:31:16.269Z + + + https://orcid.org/0000-0001-6816-8350 + 0000-0001-6816-8350 + orcid.org + + + Organizational Leadership + + + 2016-02-09T09:17:08.998Z + 2023-12-02T13:31:16.269Z + + + https://orcid.org/0000-0001-6816-8350 + 0000-0001-6816-8350 + orcid.org + + + Organizational performance + + + 2023-12-02T13:31:16.259Z + 2023-12-02T13:31:16.259Z + + + https://orcid.org/0000-0001-6816-8350 + 0000-0001-6816-8350 + orcid.org + + + Thriving at work + + + + 2018-04-10T00:49:55.386Z + + 2018-04-10T00:49:55.385Z + 2018-04-10T00:49:55.386Z + + + https://orcid.org/client/0000-0003-1377-5676 + 0000-0003-1377-5676 + orcid.org + + ResearcherID + + https://orcid.org/0000-0001-6816-8350 + 0000-0001-6816-8350 + orcid.org + + + ResearcherID + D-1929-2018 + http://www.researcherid.com/rid/D-1929-2018 + self + + + + + 2023-12-02T13:28:26.051Z + + + 2018-02-13T02:33:38.225Z + + 2016-02-09T06:55:21.838Z + + + 2016-02-09T06:54:39.199Z + 2016-02-09T06:55:21.838Z + + + https://orcid.org/0000-0001-6816-8350 + 0000-0001-6816-8350 + orcid.org + + + Management + PhD + + 2021 + + + 2022 + 02 + 12 + + + 2003 + 03 + + + 2007 + 03 + + + University of New England + + Armidale + NSW + AU + + + 1319 + RINGGOLD + + + + + + 2018-02-13T02:33:38.225Z + + + 2016-02-09T06:57:04.181Z + 2018-02-13T02:33:38.225Z + + + https://orcid.org/0000-0001-6816-8350 + 0000-0001-6816-8350 + orcid.org + + + Psychology + Master of Science (Industrial and Organizational) Psychology + + 1998 + 01 + + + 2000 + 01 + + + Universitas Gadjah Mada + + Yogyakarta + Daerah Istimewa 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https://orcid.org/client/APP-N0TAO4G9BBK9PWHT + APP-N0TAO4G9BBK9PWHT + orcid.org + + Tampere University + + + Hermosolun solunsisäisten toimintojen matemaattinen mallinnus ja simulointi + + + + source-work-id + ca0966d2-a83d-42f5-9905-b6e84115ac54 + ca0966d2-a83d-42f5-9905-b6e84115ac54 + self + + + https://researchportal.tuni.fi/en/publications/ca0966d2-a83d-42f5-9905-b6e84115ac54 + other + + 2003 + + + + -- 2.17.1 From b32a9d1994f331c1e00f0d703dc8538df85be5c6 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Fri, 23 Feb 2024 10:04:28 +0100 Subject: [PATCH 09/10] Implemented workflow for updating table , added step to check if the new generated table is valid --- .../collection/orcid/OrcidGetUpdatesFile.java | 26 +++++++++- .../download_orcid_update_parameter.json | 12 +++++ .../orcid/update/oozie_app/workflow.xml | 34 ++++++++----- .../collection/orcid/SparkApplyUpdate.scala | 49 ++++++++++++++++++- 4 files changed, 106 insertions(+), 15 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java index 2ba131e0f..c96423147 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java @@ -23,6 +23,7 @@ import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; +import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -50,6 +51,9 @@ public class OrcidGetUpdatesFile { final String namenode = parser.get("namenode"); log.info("got variable namenode: {}", namenode); + final String master = parser.get("master"); + log.info("got variable master: {}", master); + final String targetPath = parser.get("targetPath"); log.info("got variable targetPath: {}", targetPath); @@ -59,11 +63,27 @@ public class OrcidGetUpdatesFile { final String accessToken = parser.get("accessToken"); log.info("got variable accessToken: {}", accessToken); - System.out.println("namenode = " + namenode); + final String graphPath = parser.get("graphPath"); + log.info("got variable graphPath: {}", graphPath); + + final SparkSession spark = SparkSession + .builder() + .appName(OrcidGetUpdatesFile.class.getName()) + .master(master) + .getOrCreate(); + + final String latestDate = spark + .read() + .load(graphPath + "/Authors") + .selectExpr("max(lastModifiedDate)") + .first() + .getString(0); + + log.info("latest date is {}", latestDate); final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(namenode)); - new OrcidGetUpdatesFile().readTar(fileSystem, accessToken, apiURL, targetPath, "2023-09-30"); + new OrcidGetUpdatesFile().readTar(fileSystem, accessToken, apiURL, targetPath, latestDate); } @@ -102,6 +122,8 @@ public class OrcidGetUpdatesFile { Path hdfsWritePath = new Path("/tmp/orcid_updates.tar.gz"); final FSDataOutputStream fsDataOutputStream = fileSystem.create(hdfsWritePath, true); IOUtils.copy(input, fsDataOutputStream); + fsDataOutputStream.flush(); + fsDataOutputStream.close(); FSDataInputStream updateFile = fileSystem.open(hdfsWritePath); TarArchiveInputStream tais = new TarArchiveInputStream(new GzipCompressorInputStream( new BufferedInputStream( diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json index dbf63a31a..48b37f85d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json @@ -4,6 +4,12 @@ "paramDescription": "the Name Node URI", "paramRequired": true }, + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "the master name", + "paramRequired": true + }, { "paramName": "t", "paramLongName": "targetPath", @@ -16,6 +22,12 @@ "paramDescription": "the URL to download the tar file", "paramRequired": true }, + { + "paramName": "g", + "paramLongName": "graphPath", + "paramDescription": "the path of the input graph", + "paramRequired": true + }, { "paramName": "at", "paramLongName": "accessToken", 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 434d21a0c..e46e303a9 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 @@ -28,23 +28,35 @@ - - - - oozie.launcher.mapreduce.user.classpath.first - true - - - eu.dnetlib.dhp.collection.orcid.OrcidGetUpdatesFile + + yarn + cluster + Check Latest Orcid and Download updates + eu.dnetlib.dhp.collection.orcid.OrcidGetUpdatesFile + 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} + + --masteryarn --namenode${nameNode} + --graphPath${graphPath} --targetPath${targetPath} --apiURL${apiURL} --accessToken${accessToken} - - + + + yarn @@ -90,7 +102,7 @@ --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --graphPathgraphPath + --graphPath${graphPath} --updatePath${targetPath}/updateTable --targetPath${targetPath}/newTable --masteryarn diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkApplyUpdate.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkApplyUpdate.scala index 4494a2d3d..57cb0e2e4 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkApplyUpdate.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkApplyUpdate.scala @@ -19,10 +19,34 @@ class SparkApplyUpdate(propertyPath: String, args: Array[String], log: Logger) val targetPath: String = parser.get("targetPath") log.info("found parameters targetPath: {}", targetPath) applyTableUpdate(spark, graphPath, updatePath, targetPath) + checkUpdate(spark, graphPath, targetPath) + moveTable(spark, graphPath, targetPath) } - def updateDataset( + private def moveTable(spark: SparkSession, graphPath: String, updatePath: String): Unit = { + spark.read + .load(s"$updatePath/Authors") + .repartition(1000) + .write + .mode(SaveMode.Overwrite) + .save(s"$graphPath/Authors") + spark.read + .load(s"$updatePath/Works") + .repartition(1000) + .write + .mode(SaveMode.Overwrite) + .save(s"$graphPath/Works") + spark.read + .load(s"$updatePath/Employments") + .repartition(1000) + .write + .mode(SaveMode.Overwrite) + .save(s"$graphPath/Employments") + + } + + private def updateDataset( inputDataset: DataFrame, idUpdate: DataFrame, updateDataframe: DataFrame, @@ -37,7 +61,28 @@ class SparkApplyUpdate(propertyPath: String, args: Array[String], log: Logger) .save(targetPath) } - def applyTableUpdate(spark: SparkSession, graphPath: String, updatePath: String, targetPath: String) = { + private def checkUpdate(spark: SparkSession, graphPath: String, updatePath: String): Unit = { + val totalOriginalAuthors = spark.read.load(s"$graphPath/Authors").count + val totalOriginalWorks = spark.read.load(s"$graphPath/Works").count + val totalOriginalEmployments = spark.read.load(s"$graphPath/Employments").count + val totalUpdateAuthors = spark.read.load(s"$updatePath/Authors").count + val totalUpdateWorks = spark.read.load(s"$updatePath/Works").count + val totalUpdateEmployments = spark.read.load(s"$updatePath/Employments").count + + log.info("totalOriginalAuthors: {}", totalOriginalAuthors) + log.info("totalOriginalWorks: {}", totalOriginalWorks) + log.info("totalOriginalEmployments: {}", totalOriginalEmployments) + log.info("totalUpdateAuthors: {}", totalUpdateAuthors) + log.info("totalUpdateWorks: {}", totalUpdateWorks) + log.info("totalUpdateEmployments: {}", totalUpdateEmployments) + if ( + totalUpdateAuthors < totalOriginalAuthors || totalUpdateEmployments < totalOriginalEmployments || totalUpdateWorks < totalOriginalWorks + ) + throw new RuntimeException("The updated Graph contains less elements of the original one") + + } + + private def applyTableUpdate(spark: SparkSession, graphPath: String, updatePath: String, targetPath: String): Unit = { val orcidIDUpdate = spark.read.load(s"$updatePath/Authors").select("orcid") updateDataset( spark.read.load(s"$graphPath/Authors"), -- 2.17.1 From 915a76a7964e8b3fd4da8bef717d03c33209d9d2 Mon Sep 17 00:00:00 2001 From: "sandro.labruzzo" Date: Wed, 28 Feb 2024 09:10:55 +0100 Subject: [PATCH 10/10] following the comment on the pull requests: - Added #NUM_OF_THREADS complete job in the queue at the end of the main loop to avoid deadlock --- .../java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java | 1 - .../dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java | 6 ++++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java index fe59fe71f..2767a3e41 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java @@ -135,7 +135,6 @@ public class ORCIDWorker extends Thread { orcidId = queue.take(); if (orcidId.equalsIgnoreCase(JOB_COMPLETE)) { - queue.put(orcidId); hasComplete = true; } else { start = System.currentTimeMillis(); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java index c96423147..eb23a204f 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java @@ -155,15 +155,17 @@ public class OrcidGetUpdatesFile { throw new RuntimeException(e); } }); - queue.put(ORCIDWorker.JOB_COMPLETE); + } } + for (int i = 0; i < 22; i++) { + queue.put(ORCIDWorker.JOB_COMPLETE); + } for (ORCIDWorker worker : workers) { worker.join(); } - } } -- 2.17.1