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orcid-no-doi #43

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claudio.atzori merged 45 commits from enrico.ottonello/dnet-hadoop:orcid-no-doi into master 2020-12-02 10:55:12 +01:00
Conversation 5 Commits 45 Files Changed 68 +320 -228
20 changed files with 320 additions and 228 deletions
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2
dhp-workflows/dhp-doiboost/pom.xml
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@ -51,7 +51,6 @@
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>${org.apache.httpcomponents.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
@ -87,7 +86,6 @@
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>${common.text.version}</version>
</dependency>
claudio.atzori commented 2020-09-16 09:56:50 +02:00
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Versions of dependencies should be only declared in the main pom file. Please declare this dependency there (v1.8) and refer to it without overriding the version.

Versions of dependencies should be only declared in the main pom file. Please declare this dependency there (v1.8) and refer to it without overriding the version.
claudio.atzori commented 2020-09-22 11:10:54 +02:00
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Please remove the dependency version at all from here. The version has to be declared only in the main pom file. Just like all the other dependencies in the same pom file.

Please remove the dependency version at all from here. The version has to be declared *only* in the main pom file. Just like all the other dependencies in the same pom file.
claudio.atzori commented 2020-11-03 17:02:04 +01:00
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I still see the dependency version declared here. Please move in the project's main pom under the dependencyManagement section.

I still see the dependency version declared here. Please move in the project's main pom under the _dependencyManagement_ section.

2
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java
View File

@ -62,7 +62,7 @@ public class OrcidDSManager {
.toString(
OrcidDSManager.class
.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json")));
"/eu/dnetlib/dhp/doiboost/gen_orcid_authors_from_summaries.json")));
parser.parseArgument(args);
hdfsServerUri = parser.get("hdfsServerUri");

4
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/ActivitiesDumpReader.java
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@ -73,7 +73,7 @@ public class ActivitiesDumpReader {
SequenceFile.Writer.valueClass(Text.class))) {
while ((entry = tais.getNextTarEntry()) != null) {
String filename = entry.getName();
StringBuffer buffer = new StringBuffer();
try {
if (entry.isDirectory() || !filename.contains("works")) {
@ -83,7 +83,7 @@ public class ActivitiesDumpReader {
BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from
// tarInput
String line;
StringBuffer buffer = new StringBuffer();
buffer = new StringBuffer();
while ((line = br.readLine()) != null) {
buffer.append(line);
}

2
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/GenOrcidAuthorWork.java
View File

@ -42,7 +42,7 @@ public class GenOrcidAuthorWork extends OrcidDSManager {
.toString(
GenOrcidAuthorWork.class
.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_parameters.json")));
"/eu/dnetlib/dhp/doiboost/gen_orcid_works-no-doi_from_activities.json")));
parser.parseArgument(args);
hdfsServerUri = parser.get("hdfsServerUri");

8
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java
View File

@ -67,7 +67,7 @@ public class SparkGenEnrichedOrcidWorks {
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaPairRDD<Text, Text> summariesRDD = sc
.sequenceFile(workingPath + "summaries/output/authors.seq", Text.class, Text.class);
.sequenceFile(workingPath + "authors/authors.seq", Text.class, Text.class);
Dataset<AuthorData> summariesDataset = spark
.createDataset(
summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(),
@ -96,8 +96,8 @@ public class SparkGenEnrichedOrcidWorks {
Encoders.tuple(Encoders.STRING(), Encoders.STRING()))
.filter(Objects::nonNull)
.toJavaRDD();
enrichedWorksRDD.saveAsTextFile(workingPath + outputEnrichedWorksPath);
logger.info("Works enriched data saved");
// enrichedWorksRDD.saveAsTextFile(workingPath + outputEnrichedWorksPath);
logger.info("Enriched works RDD ready.");
final LongAccumulator parsedPublications = spark.sparkContext().longAccumulator("parsedPublications");
final LongAccumulator enrichedPublications = spark
@ -132,7 +132,7 @@ public class SparkGenEnrichedOrcidWorks {
.write()
.format("parquet")
.mode(SaveMode.Overwrite)
.save(workingPath + "no_doi_dataset/output");
.save(workingPath + outputEnrichedWorksPath);
logger.info("parsedPublications: " + parsedPublications.value().toString());
logger.info("enrichedPublications: " + enrichedPublications.value().toString());

4
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/similarity/AuthorMatcher.java
View File

@ -5,6 +5,7 @@ import java.io.IOException;
import java.text.Normalizer;
import java.util.*;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.text.similarity.JaroWinklerSimilarity;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -40,7 +41,7 @@ public class AuthorMatcher {
int matchCounter = 0;
List<Integer> matchCounters = Arrays.asList(matchCounter);
Contributor contributor = null;
contributors.forEach(c -> {
contributors.stream().filter(c -> !StringUtils.isBlank(c.getCreditName())).forEach(c -> {
if (simpleMatch(c.getCreditName(), author.getName()) ||
simpleMatch(c.getCreditName(), author.getSurname()) ||
simpleMatch(c.getCreditName(), author.getOtherName())) {
@ -54,6 +55,7 @@ public class AuthorMatcher {
Optional<Contributor> optCon = contributors
.stream()
.filter(c -> c.isSimpleMatch())
.filter(c -> !StringUtils.isBlank(c.getCreditName()))
.map(c -> {
c.setScore(bestMatch(author.getName(), author.getSurname(), c.getCreditName()));
return c;

45
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/xml/XMLRecordParserNoDoi.java
View File

@ -183,39 +183,34 @@ public class XMLRecordParserNoDoi {
private static List<Contributor> getContributors(VTDGen vg, VTDNav vn, AutoPilot ap)
throws XPathParseException, NavException, XPathEvalException {
List<Contributor> contributors = new ArrayList<Contributor>();
int nameIndex = 0;
ap.selectXPath("//work:contributor/work:credit-name");
ap.selectXPath("//work:contributors/work:contributor");
while (ap.evalXPath() != -1) {
Contributor contributor = new Contributor();
int t = vn.getText();
if (t >= 0) {
contributor.setCreditName(vn.toNormalizedString(t));
contributors.add(nameIndex, contributor);
nameIndex++;
if (vn.toElement(VTDNav.FIRST_CHILD, "work:credit-name")) {
int val = vn.getText();
if (val != -1) {
contributor.setCreditName(vn.toNormalizedString(val));
}
vn.toElement(VTDNav.PARENT);
}
if (contributors.size() == 0) {
return contributors;
if (vn.toElement(VTDNav.FIRST_CHILD, "work:contributor-attributes")) {
if (vn.toElement(VTDNav.FIRST_CHILD, "work:contributor-sequence")) {
int val = vn.getText();
if (val != -1) {
contributor.setSequence(vn.toNormalizedString(val));
}
int sequenceIndex = 0;
ap.selectXPath("//work:contributor/work:contributor-attributes/work:contributor-sequence");
while (ap.evalXPath() != -1) {
int t = vn.getText();
if (t >= 0) {
contributors.get(sequenceIndex).setSequence(vn.toNormalizedString(t));
sequenceIndex++;
vn.toElement(VTDNav.PARENT);
}
if (vn.toElement(VTDNav.FIRST_CHILD, "work:contributor-role")) {
int val = vn.getText();
if (val != -1) {
contributor.setRole(vn.toNormalizedString(val));
}
int roleIndex = 0;
ap.selectXPath("//work:contributor/work:contributor-attributes/work:contributor-role");
while (ap.evalXPath() != -1) {
int t = vn.getText();
if (t >= 0) {
contributors.get(roleIndex).setRole(vn.toNormalizedString(t));
roleIndex++;
vn.toElement(VTDNav.PARENT);
}
vn.toElement(VTDNav.PARENT);
}
contributors.add(contributor);
}
return contributors;
}

0
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json → dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_from_summaries.json
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7
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_works-no-doi_from_activities.json Normal file
View File

@ -0,0 +1,7 @@
[
{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true},
{"paramName":"f", "paramLongName":"activitiesFileNameTarGz", "paramDescription": "the name of the activities orcid file", "paramRequired": true},
{"paramName":"ow", "paramLongName":"outputWorksPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true},
{"paramName":"oew", "paramLongName":"outputEnrichedWorksPath", "paramDescription": "the relative folder of the sequencial file to write the data", "paramRequired": true}
]

42
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml
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@ -1,42 +0,0 @@
<configuration>
<property>
<name>jobTracker</name>
<value>hadoop-rm3.garr-pa1.d4science.org:8032</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://hadoop-rm1.garr-pa1.d4science.org:8020</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://hadoop-edge2.garr-pa1.d4science.org:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://hadoop-edge1.garr-pa1.d4science.org:18089/</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
</property>
</configuration>

67
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml
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@ -1,67 +0,0 @@
<workflow-app name="Import Orcid Summaries" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPath</name>
<description>the working dir base path</description>
</property>
<property>
<name>shell_cmd_0</name>
<value>wget -O /tmp/ORCID_2019_summaries.tar.gz https://orcid.figshare.com/ndownloader/files/18017633 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_summaries.tar.gz /data/orcid_activities/ORCID_2019_summaries.tar.gz ; rm -f /tmp/ORCID_2019_summaries.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid summaries</description>
</property>
</parameters>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${workingPath}/summaries/output'/>
<mkdir path='${workingPath}/summaries/output'/>
</fs>
<ok to="check_exist_on_hdfs_summaries"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_summaries">
<switch>
<case to="ImportOrcidSummaries">
${fs:exists(concat(workingPath,'/ORCID_2019_summaries.tar.gz'))}
</case>
<default to="DownloadSummaries" />
</switch>
</decision>
<action name="DownloadSummaries">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_0}</argument>
<capture-output/>
</shell>
<ok to="ImportOrcidSummaries"/>
<error to="Kill"/>
</action>
<action name="ImportOrcidSummaries">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidDSManager</main-class>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_summaries.tar.gz</arg>
<arg>-o</arg><arg>summaries/output/</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

2
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/config-default.xml
View File

@ -9,7 +9,7 @@
</property>
<property>
<name>oozie.launcher.mapreduce.map.java.opts</name>
<value>-Xmx4g</value>
<value>-Xmx2g</value>
</property>
<property>
<name>jobTracker</name>

144
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_activities/oozie_app/workflow.xml
View File

@ -1,4 +1,4 @@
<workflow-app name="Import Orcid Activities" xmlns="uri:oozie:workflow:0.5">
<workflow-app name="Gen Orcid Works-no-doi From Activities" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPath</name>
@ -6,67 +6,67 @@
</property>
<property>
<name>shell_cmd_0</name>
<value>wget -O /tmp/ORCID_2019_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/18017660 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_0.tar.gz /data/orcid_activities/ORCID_2019_activites_0.tar.gz ; rm -f /tmp/ORCID_2019_activites_0.tar.gz
<value>wget -O /tmp/ORCID_2020_10_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/25002232 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_0.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_0.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_0.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 0</description>
</property>
<property>
<name>shell_cmd_1</name>
<value>wget -O /tmp/ORCID_2019_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/18017675 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_1.tar.gz /data/orcid_activities/ORCID_2019_activites_1.tar.gz ; rm -f /tmp/ORCID_2019_activites_1.tar.gz
<value>wget -O /tmp/ORCID_2020_10_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/25002088 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_1.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_1.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_1.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 1</description>
</property>
<property>
<name>shell_cmd_2</name>
<value>wget -O /tmp/ORCID_2019_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/18017717 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_2.tar.gz /data/orcid_activities/ORCID_2019_activites_2.tar.gz ; rm -f /tmp/ORCID_2019_activites_2.tar.gz
<value>wget -O /tmp/ORCID_2020_10_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/25000596 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_2.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_2.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_2.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 2</description>
</property>
<property>
<name>shell_cmd_3</name>
<value>wget -O /tmp/ORCID_2019_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/18017765 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_3.tar.gz /data/orcid_activities/ORCID_2019_activites_3.tar.gz ; rm -f /tmp/ORCID_2019_activites_3.tar.gz
<value>wget -O /tmp/ORCID_2020_10_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/25015150 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_3.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_3.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_3.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 3</description>
</property>
<property>
<name>shell_cmd_4</name>
<value>wget -O /tmp/ORCID_2019_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/18017831 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_4.tar.gz /data/orcid_activities/ORCID_2019_activites_4.tar.gz ; rm -f /tmp/ORCID_2019_activites_4.tar.gz
<value>wget -O /tmp/ORCID_2020_10_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/25033643 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_4.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_4.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_4.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 4</description>
</property>
<property>
<name>shell_cmd_5</name>
<value>wget -O /tmp/ORCID_2019_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/18017987 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_5.tar.gz /data/orcid_activities/ORCID_2019_activites_5.tar.gz ; rm -f /tmp/ORCID_2019_activites_5.tar.gz
<value>wget -O /tmp/ORCID_2020_10_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/25005483 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_5.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_5.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_5.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 5</description>
</property>
<property>
<name>shell_cmd_6</name>
<value>wget -O /tmp/ORCID_2019_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/18018053 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_6.tar.gz /data/orcid_activities/ORCID_2019_activites_6.tar.gz ; rm -f /tmp/ORCID_2019_activites_6.tar.gz
<value>wget -O /tmp/ORCID_2020_10_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/25005425 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_6.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_6.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_6.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 6</description>
</property>
<property>
<name>shell_cmd_7</name>
<value>wget -O /tmp/ORCID_2019_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/18018023 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_7.tar.gz /data/orcid_activities/ORCID_2019_activites_7.tar.gz ; rm -f /tmp/ORCID_2019_activites_7.tar.gz
<value>wget -O /tmp/ORCID_2020_10_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/25012016 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_7.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_7.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_7.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 7</description>
</property>
<property>
<name>shell_cmd_8</name>
<value>wget -O /tmp/ORCID_2019_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/18018248 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_8.tar.gz /data/orcid_activities/ORCID_2019_activites_8.tar.gz ; rm -f /tmp/ORCID_2019_activites_8.tar.gz
<value>wget -O /tmp/ORCID_2020_10_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/25012079 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_8.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_8.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_8.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 8</description>
</property>
<property>
<name>shell_cmd_9</name>
<value>wget -O /tmp/ORCID_2019_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/18018029 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_9.tar.gz /data/orcid_activities/ORCID_2019_activites_9.tar.gz ; rm -f /tmp/ORCID_2019_activites_9.tar.gz
<value>wget -O /tmp/ORCID_2020_10_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/25010727 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_9.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_9.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_9.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 9</description>
</property>
<property>
<name>shell_cmd_X</name>
<value>wget -O /tmp/ORCID_2019_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/18018182 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_X.tar.gz /data/orcid_activities/ORCID_2019_activites_X.tar.gz ; rm -f /tmp/ORCID_2019_activites_X.tar.gz
<value>wget -O /tmp/ORCID_2020_10_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/25011025 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_activites_X.tar.gz /data/orcid_activities_2020/ORCID_2020_10_activites_X.tar.gz ; rm -f /tmp/ORCID_2020_10_activites_X.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file X</description>
</property>
@ -82,11 +82,11 @@
<fs>
<delete path='${workingPath}/no_doi_works/*'/>
</fs>
<ok to="fork_gen_orcid_author_work"/>
<ok to="fork_check_download_files"/>
<error to="Kill"/>
</action>
<fork name = "fork_gen_orcid_author_work">
<fork name = "fork_check_download_files">
<path start = "check_exist_on_hdfs_activities_0"/>
<path start = "check_exist_on_hdfs_activities_1"/>
<path start = "check_exist_on_hdfs_activities_2"/>
@ -102,8 +102,8 @@
<decision name="check_exist_on_hdfs_activities_0">
<switch>
<case to="GenOrcidAuthorWork_0">
${fs:exists(concat(workingPath,'/ORCID_2019_activites_0.tar.gz'))}
<case to="wait_download_phase_node">
${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_0.tar.gz'))}
</case>
<default to="Download_0" />
</switch>
@ -118,7 +118,7 @@
<argument>${shell_cmd_0}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_0"/>
<ok to="wait_download_phase_node"/>
<error to="Kill"/>
</action>
@ -129,7 +129,7 @@
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_0.tar.gz</arg>
<arg>-f</arg><arg>ORCID_2020_10_activites_0.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_0.seq</arg>
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
</java>
@ -139,8 +139,8 @@
<decision name="check_exist_on_hdfs_activities_1">
<switch>
<case to="GenOrcidAuthorWork_1">
${fs:exists(concat(workingPath,'/ORCID_2019_activites_1.tar.gz'))}
<case to="wait_download_phase_node">
${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_1.tar.gz'))}
</case>
<default to="Download_1" />
</switch>
@ -155,7 +155,7 @@
<argument>${shell_cmd_1}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_1"/>
<ok to="wait_download_phase_node"/>
<error to="Kill"/>
</action>
@ -166,7 +166,7 @@
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_1.tar.gz</arg>
<arg>-f</arg><arg>ORCID_2020_10_activites_1.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_1.seq</arg>
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
</java>
@ -176,8 +176,8 @@
<decision name="check_exist_on_hdfs_activities_2">
<switch>
<case to="GenOrcidAuthorWork_2">
${fs:exists(concat(workingPath,'/ORCID_2019_activites_2.tar.gz'))}
<case to="wait_download_phase_node">
${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_2.tar.gz'))}
</case>
<default to="Download_2" />
</switch>
@ -192,7 +192,7 @@
<argument>${shell_cmd_2}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_2"/>
<ok to="wait_download_phase_node"/>
<error to="Kill"/>
</action>
@ -203,7 +203,7 @@
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_2.tar.gz</arg>
<arg>-f</arg><arg>ORCID_2020_10_activites_2.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_2.seq</arg>
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
</java>
@ -213,8 +213,8 @@
<decision name="check_exist_on_hdfs_activities_3">
<switch>
<case to="GenOrcidAuthorWork_3">
${fs:exists(concat(workingPath,'/ORCID_2019_activites_3.tar.gz'))}
<case to="wait_download_phase_node">
${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_3.tar.gz'))}
</case>
<default to="Download_3" />
</switch>
@ -229,7 +229,7 @@
<argument>${shell_cmd_3}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_3"/>
<ok to="wait_download_phase_node"/>
<error to="Kill"/>
</action>
@ -240,7 +240,7 @@
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_3.tar.gz</arg>
<arg>-f</arg><arg>ORCID_2020_10_activites_3.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_3.seq</arg>
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
</java>
@ -250,8 +250,8 @@
<decision name="check_exist_on_hdfs_activities_4">
<switch>
<case to="GenOrcidAuthorWork_4">
${fs:exists(concat(workingPath,'/ORCID_2019_activites_4.tar.gz'))}
<case to="wait_download_phase_node">
${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_4.tar.gz'))}
</case>
<default to="Download_4" />
</switch>
@ -266,7 +266,7 @@
<argument>${shell_cmd_4}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_4"/>
<ok to="wait_download_phase_node"/>
<error to="Kill"/>
</action>
@ -277,7 +277,7 @@
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_4.tar.gz</arg>
<arg>-f</arg><arg>ORCID_2020_10_activites_4.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_4.seq</arg>
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
</java>
@ -287,8 +287,8 @@
<decision name="check_exist_on_hdfs_activities_5">
<switch>
<case to="GenOrcidAuthorWork_5">
${fs:exists(concat(workingPath,'/ORCID_2019_activites_5.tar.gz'))}
<case to="wait_download_phase_node">
${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_5.tar.gz'))}
</case>
<default to="Download_5" />
</switch>
@ -303,7 +303,7 @@
<argument>${shell_cmd_5}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_5"/>
<ok to="wait_download_phase_node"/>
<error to="Kill"/>
</action>
@ -314,7 +314,7 @@
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_5.tar.gz</arg>
<arg>-f</arg><arg>ORCID_2020_10_activites_5.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_5.seq</arg>
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
</java>
@ -324,8 +324,8 @@
<decision name="check_exist_on_hdfs_activities_6">
<switch>
<case to="GenOrcidAuthorWork_6">
${fs:exists(concat(workingPath,'/ORCID_2019_activites_6.tar.gz'))}
<case to="wait_download_phase_node">
${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_6.tar.gz'))}
</case>
<default to="Download_6" />
</switch>
@ -340,7 +340,7 @@
<argument>${shell_cmd_6}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_6"/>
<ok to="wait_download_phase_node"/>
<error to="Kill"/>
</action>
@ -351,7 +351,7 @@
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_6.tar.gz</arg>
<arg>-f</arg><arg>ORCID_2020_10_activites_6.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_6.seq</arg>
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
</java>
@ -362,8 +362,8 @@
<decision name="check_exist_on_hdfs_activities_7">
<switch>
<case to="GenOrcidAuthorWork_7">
${fs:exists(concat(workingPath,'/ORCID_2019_activites_7.tar.gz'))}
<case to="wait_download_phase_node">
${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_7.tar.gz'))}
</case>
<default to="Download_7" />
</switch>
@ -378,7 +378,7 @@
<argument>${shell_cmd_7}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_7"/>
<ok to="wait_download_phase_node"/>
<error to="Kill"/>
</action>
@ -389,7 +389,7 @@
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_7.tar.gz</arg>
<arg>-f</arg><arg>ORCID_2020_10_activites_7.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_7.seq</arg>
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
</java>
@ -399,8 +399,8 @@
<decision name="check_exist_on_hdfs_activities_8">
<switch>
<case to="GenOrcidAuthorWork_8">
${fs:exists(concat(workingPath,'/ORCID_2019_activites_8.tar.gz'))}
<case to="wait_download_phase_node">
${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_8.tar.gz'))}
</case>
<default to="Download_8" />
</switch>
@ -415,7 +415,7 @@
<argument>${shell_cmd_8}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_8"/>
<ok to="wait_download_phase_node"/>
<error to="Kill"/>
</action>
@ -426,7 +426,7 @@
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_8.tar.gz</arg>
<arg>-f</arg><arg>ORCID_2020_10_activites_8.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_8.seq</arg>
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
</java>
@ -436,8 +436,8 @@
<decision name="check_exist_on_hdfs_activities_9">
<switch>
<case to="GenOrcidAuthorWork_9">
${fs:exists(concat(workingPath,'/ORCID_2019_activites_9.tar.gz'))}
<case to="wait_download_phase_node">
${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_9.tar.gz'))}
</case>
<default to="Download_9" />
</switch>
@ -452,7 +452,7 @@
<argument>${shell_cmd_9}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_9"/>
<ok to="wait_download_phase_node"/>
<error to="Kill"/>
</action>
@ -463,7 +463,7 @@
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_9.tar.gz</arg>
<arg>-f</arg><arg>ORCID_2020_10_activites_9.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_9.seq</arg>
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
</java>
@ -473,8 +473,8 @@
<decision name="check_exist_on_hdfs_activities_X">
<switch>
<case to="GenOrcidAuthorWork_X">
${fs:exists(concat(workingPath,'/ORCID_2019_activites_X.tar.gz'))}
<case to="wait_download_phase_node">
${fs:exists(concat(workingPath,'/ORCID_2020_10_activites_X.tar.gz'))}
</case>
<default to="Download_X" />
</switch>
@ -489,7 +489,7 @@
<argument>${shell_cmd_X}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_X"/>
<ok to="wait_download_phase_node"/>
<error to="Kill"/>
</action>
@ -500,7 +500,7 @@
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_X.tar.gz</arg>
<arg>-f</arg><arg>ORCID_2020_10_activites_X.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_X.seq</arg>
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
</java>
@ -508,7 +508,35 @@
<error to="Kill"/>
</action>
<join name = "wait_download_phase_node" to = "fork_gen_orcid_author_work"/>
<fork name = "fork_gen_orcid_author_work">
<path start = "GenOrcidAuthorWork_0"/>
<path start = "GenOrcidAuthorWork_1"/>
<path start = "GenOrcidAuthorWork_2"/>
<path start = "GenOrcidAuthorWork_3"/>
<path start = "GenOrcidAuthorWork_4"/>
<path start = "GenOrcidAuthorWork_5"/>
<path start = "GenOrcidAuthorWork_6"/>
<path start = "GenOrcidAuthorWork_7"/>
<path start = "GenOrcidAuthorWork_8"/>
<path start = "GenOrcidAuthorWork_9"/>
<path start = "GenOrcidAuthorWork_X"/>
</fork>
<join name = "join_node" to = "End"/>
<!-- <join name = "join_node" to = "fork_gen_orcid_author_work_2"/>-->
<!-- <fork name = "fork_gen_orcid_author_work_2">-->
<!-- <path start = "GenOrcidAuthorWork_6"/>-->
<!-- <path start = "GenOrcidAuthorWork_7"/>-->
<!-- <path start = "GenOrcidAuthorWork_8"/>-->
<!-- <path start = "GenOrcidAuthorWork_9"/>-->
<!-- <path start = "GenOrcidAuthorWork_X"/>-->
<!-- </fork>-->
<!-- <join name = "join_node_2" to = "End"/>-->
<end name="End"/>
</workflow-app>

4
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/config-default.xml
View File

@ -19,4 +19,8 @@
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
<property>
<name>oozie.launcher.mapreduce.map.java.opts</name>
<value>-Xmx16g</value>
</property>
</configuration>

14
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_summaries/oozie_app/workflow.xml
View File

@ -1,4 +1,4 @@
<workflow-app name="Import Orcid Summaries" xmlns="uri:oozie:workflow:0.5">
<workflow-app name="Gen Orcid Authors From Summaries" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPath</name>
@ -6,7 +6,7 @@
</property>
<property>
<name>shell_cmd_0</name>
<value>wget -O /tmp/ORCID_2019_summaries.tar.gz https://orcid.figshare.com/ndownloader/files/18017633 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_summaries.tar.gz /data/orcid_activities/ORCID_2019_summaries.tar.gz ; rm -f /tmp/ORCID_2019_summaries.tar.gz
<value>wget -O /tmp/ORCID_2020_10_summaries.tar.gz https://orcid.figshare.com/ndownloader/files/25032905 ; hdfs dfs -copyFromLocal /tmp/ORCID_2020_10_summaries.tar.gz /data/orcid_activities_2020/ORCID_2020_10_summaries.tar.gz ; rm -f /tmp/ORCID_2020_10_summaries.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid summaries</description>
</property>
@ -21,8 +21,8 @@
<action name="ResetWorkingPath">
<fs>
<delete path='${workingPath}/summaries/output'/>
<mkdir path='${workingPath}/summaries/output'/>
<delete path='${workingPath}/authors'/>
<mkdir path='${workingPath}/authors'/>
</fs>
<ok to="check_exist_on_hdfs_summaries"/>
<error to="Kill"/>
@ -31,7 +31,7 @@
<decision name="check_exist_on_hdfs_summaries">
<switch>
<case to="ImportOrcidSummaries">
${fs:exists(concat(workingPath,'/ORCID_2019_summaries.tar.gz'))}
${fs:exists(concat(workingPath,'/ORCID_2020_10_summaries.tar.gz'))}
</case>
<default to="DownloadSummaries" />
</switch>
@ -57,8 +57,8 @@
<main-class>eu.dnetlib.doiboost.orcid.OrcidDSManager</main-class>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_summaries.tar.gz</arg>
<arg>-o</arg><arg>summaries/output/</arg>
<arg>-f</arg><arg>ORCID_2020_10_summaries.tar.gz</arg>
<arg>-o</arg><arg>authors/</arg>
</java>
<ok to="End"/>
<error to="Kill"/>

4
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works/oozie_app/workflow.xml → dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcidnodoi/oozie_app/workflow.xml
View File

@ -59,7 +59,7 @@
<action name="ResetWorkingPath">
<fs>
<delete path='${workingPath}/no_doi_enriched_works/output'/>
<delete path='${workingPath}/no_doi_dataset'/>
</fs>
<ok to="GenOrcidNoDoiDataset"/>
<error to="Kill"/>
@ -85,7 +85,7 @@
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>-</arg>
<arg>-ow</arg><arg>no_doi_works/</arg>
<arg>-oew</arg><arg>no_doi_enriched_works/output</arg>
<arg>-oew</arg><arg>no_doi_dataset</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>

4
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java
View File

@ -38,8 +38,8 @@ public class OrcidClientTest {
@Test
public void downloadTest() throws Exception {
String record = testDownloadRecord("0000-0002-2536-4498");
File f = new File("/tmp/downloaded_0000-0002-2536-4498.xml");
String record = testDownloadRecord("0000-0001-6163-2042");
File f = new File("/tmp/downloaded_0000-0001-6163-2042.xml");
OutputStream outStream = new FileOutputStream(f);
IOUtils.write(record.getBytes(), outStream);
System.out.println("saved to tmp");

60
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/xml/OrcidNoDoiTest.java
View File

@ -2,15 +2,20 @@
package eu.dnetlib.doiboost.orcidnodoi.xml;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.IOException;
import java.text.Normalizer;
import java.util.*;
import javax.validation.constraints.AssertTrue;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.text.similarity.JaccardSimilarity;
import org.apache.commons.text.similarity.JaroWinklerSimilarity;
import org.junit.jupiter.api.Test;
import org.mortbay.log.Log;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -41,7 +46,6 @@ public class OrcidNoDoiTest {
String orcidIdA = "0000-0003-2760-1191";
@Test
// @Ignore
public void readPublicationFieldsTest()
throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException {
logger.info("running loadPublicationFieldsTest ....");
@ -95,8 +99,7 @@ public class OrcidNoDoiTest {
}
@Test
// @Ignore
private void authorMatchTest() throws Exception {
public void authorMatchTest() throws Exception {
logger.info("running authorSimpleMatchTest ....");
String orcidWork = "activity_work_0000-0003-2760-1191-similarity.xml";
AuthorData author = new AuthorData();
@ -121,9 +124,60 @@ public class OrcidNoDoiTest {
logger.error("parsing xml", e);
}
assertNotNull(workData);
Contributor a = workData.getContributors().get(0);
assertTrue(a.getCreditName().equals("Abdel-Dayem K"));
AuthorMatcher.match(author, workData.getContributors());
GsonBuilder builder = new GsonBuilder();
Gson gson = builder.create();
logger.info(gson.toJson(workData));
assertTrue(workData.getContributors().size() == 6);
Contributor c = workData.getContributors().get(0);
assertTrue(c.getOid().equals("0000-0003-2760-1191"));
assertTrue(c.getName().equals("Khairy"));
assertTrue(c.getSurname().equals("Abdel Dayem"));
assertTrue(c.getCreditName().equals("Abdel-Dayem K"));
}
@Test
public void readContributorsTest()
throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException {
logger.info("running loadPublicationFieldsTest ....");
String xml = IOUtils
.toString(
OrcidNoDoiTest.class.getResourceAsStream("activity_work_0000-0003-2760-1191_contributors.xml"));
if (xml == null) {
logger.info("Resource not found");
}
XMLRecordParserNoDoi p = new XMLRecordParserNoDoi();
if (p == null) {
logger.info("XMLRecordParserNoDoi null");
}
WorkDataNoDoi workData = null;
try {
workData = p.VTDParseWorkData(xml.getBytes());
} catch (Exception e) {
logger.error("parsing xml", e);
}
assertNotNull(workData.getContributors());
assertTrue(workData.getContributors().size() == 5);
assertTrue(StringUtils.isBlank(workData.getContributors().get(0).getCreditName()));
assertTrue(workData.getContributors().get(0).getSequence().equals("seq0"));
assertTrue(workData.getContributors().get(0).getRole().equals("role0"));
assertTrue(workData.getContributors().get(1).getCreditName().equals("creditname1"));
assertTrue(StringUtils.isBlank(workData.getContributors().get(1).getSequence()));
assertTrue(StringUtils.isBlank(workData.getContributors().get(1).getRole()));
assertTrue(workData.getContributors().get(2).getCreditName().equals("creditname2"));
assertTrue(workData.getContributors().get(2).getSequence().equals("seq2"));
assertTrue(StringUtils.isBlank(workData.getContributors().get(2).getRole()));
assertTrue(workData.getContributors().get(3).getCreditName().equals("creditname3"));
assertTrue(StringUtils.isBlank(workData.getContributors().get(3).getSequence()));
assertTrue(workData.getContributors().get(3).getRole().equals("role3"));
assertTrue(StringUtils.isBlank(workData.getContributors().get(4).getCreditName()));
assertTrue(workData.getContributors().get(4).getSequence().equals("seq4"));
assertTrue(workData.getContributors().get(4).getRole().equals("role4"));
}
}

101
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcidnodoi/xml/activity_work_0000-0003-2760-1191_contributors.xml Normal file
View File

@ -0,0 +1,101 @@
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<work:work xmlns:address="http://www.orcid.org/ns/address"
xmlns:email="http://www.orcid.org/ns/email" xmlns:history="http://www.orcid.org/ns/history"
xmlns:employment="http://www.orcid.org/ns/employment"
xmlns:education="http://www.orcid.org/ns/education"
xmlns:other-name="http://www.orcid.org/ns/other-name"
xmlns:deprecated="http://www.orcid.org/ns/deprecated"
xmlns:funding="http://www.orcid.org/ns/funding"
xmlns:research-resource="http://www.orcid.org/ns/research-resource"
xmlns:service="http://www.orcid.org/ns/service"
xmlns:researcher-url="http://www.orcid.org/ns/researcher-url"
xmlns:distinction="http://www.orcid.org/ns/distinction"
xmlns:internal="http://www.orcid.org/ns/internal"
xmlns:membership="http://www.orcid.org/ns/membership"
xmlns:person="http://www.orcid.org/ns/person"
xmlns:personal-details="http://www.orcid.org/ns/personal-details"
xmlns:bulk="http://www.orcid.org/ns/bulk" xmlns:common="http://www.orcid.org/ns/common"
xmlns:record="http://www.orcid.org/ns/record" xmlns:keyword="http://www.orcid.org/ns/keyword"
xmlns:activities="http://www.orcid.org/ns/activities"
xmlns:qualification="http://www.orcid.org/ns/qualification"
xmlns:external-identifier="http://www.orcid.org/ns/external-identifier"
xmlns:error="http://www.orcid.org/ns/error"
xmlns:preferences="http://www.orcid.org/ns/preferences"
xmlns:invited-position="http://www.orcid.org/ns/invited-position"
xmlns:work="http://www.orcid.org/ns/work"
xmlns:peer-review="http://www.orcid.org/ns/peer-review" put-code="28776099"
path="/0000-0003-2760-1191/work/28776099" visibility="public">
<common:created-date>2016-12-12T23:02:05.233Z</common:created-date>
<common:last-modified-date>2016-12-13T09:08:16.412Z</common:last-modified-date>
<common:source>
<common:source-orcid>
<common:uri>https://orcid.org/0000-0002-9157-3431</common:uri>
<common:path>0000-0002-9157-3431</common:path>
<common:host>orcid.org</common:host>
</common:source-orcid>
<common:source-name>Europe PubMed Central</common:source-name>
</common:source>
<work:title>
<common:title>Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which
Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for
ST-Segment-Elevation Myocardial Infarction.</common:title>
</work:title>
<work:citation>
<work:citation-type>formatted-unspecified</work:citation-type>
<work:citation-value>Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta
Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016</work:citation-value>
</work:citation>
<work:type>journal-article</work:type>
<common:publication-date>
<common:year>2016</common:year>
<common:month>11</common:month>
</common:publication-date>
<common:external-ids>
<common:external-id>
<common:external-id-type>pmid</common:external-id-type>
<common:external-id-value>27899851</common:external-id-value>
<common:external-id-normalized transient="true">27899851</common:external-id-normalized>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
<common:external-id>
<common:external-id-type>pmc</common:external-id-type>
<common:external-id-value>PMC5126442</common:external-id-value>
<common:external-id-normalized transient="true"
>PMC5126442</common:external-id-normalized>
<common:external-id-relationship>self</common:external-id-relationship>
</common:external-id>
</common:external-ids>
<common:url>http://europepmc.org/abstract/med/27899851</common:url>
<work:contributors>
<work:contributor>
<work:contributor-attributes>
<work:contributor-sequence>seq0</work:contributor-sequence>
<work:contributor-role>role0</work:contributor-role>
</work:contributor-attributes>
</work:contributor>
<work:contributor>
<work:credit-name>creditname1</work:credit-name>
</work:contributor>
<work:contributor>
<work:credit-name>creditname2</work:credit-name>
<work:contributor-attributes>
<work:contributor-sequence>seq2</work:contributor-sequence>
<work:contributor-role></work:contributor-role>
</work:contributor-attributes>
</work:contributor>
<work:contributor>
<work:credit-name>creditname3</work:credit-name>
<work:contributor-attributes>
<work:contributor-sequence></work:contributor-sequence>
<work:contributor-role>role3</work:contributor-role>
</work:contributor-attributes>
</work:contributor>
<work:contributor>
<work:credit-name></work:credit-name>
<work:contributor-attributes>
<work:contributor-sequence>seq4</work:contributor-sequence>
<work:contributor-role>role4</work:contributor-role>
</work:contributor-attributes>
</work:contributor>
</work:contributors>
</work:work>

12
pom.xml
View File

@ -458,6 +458,18 @@
<version>${jsonschemagenerator.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>${common.text.version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>${org.apache.httpcomponents.version}</version>
</dependency>
</dependencies>
</dependencyManagement>