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Change the access right in DoiBoost #126

Merged
claudio.atzori merged 19 commits from doiboosi_accessright into beta 2021-07-28 11:29:15 +02:00
Conversation 0 Commits 19 Files Changed 10 +264 -694
15 changed files with 264 additions and 694 deletions
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17
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkConvertORCIDToOAF.scala
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@ -10,6 +10,16 @@ import org.slf4j.{Logger, LoggerFactory}
object SparkConvertORCIDToOAF { object SparkConvertORCIDToOAF {
val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass) val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass)
def run(spark:SparkSession, workingPath:String, targetPath:String) :Unit = {
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
import spark.implicits._
val dataset: Dataset[ORCIDItem] =spark.read.load(s"$workingPath/orcidworksWithAuthor").as[ORCIDItem]
logger.info("Converting ORCID to OAF")
dataset.map(o => ORCIDToOAF.convertTOOAF(o)).write.mode(SaveMode.Overwrite).save(targetPath)
}
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
val conf: SparkConf = new SparkConf() val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_orcid_to_oaf_params.json"))) val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_orcid_to_oaf_params.json")))
@ -21,16 +31,11 @@ object SparkConvertORCIDToOAF {
.appName(getClass.getSimpleName) .appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate() .master(parser.get("master")).getOrCreate()
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
import spark.implicits._
val workingPath = parser.get("workingPath") val workingPath = parser.get("workingPath")
val targetPath = parser.get("targetPath") val targetPath = parser.get("targetPath")
val dataset: Dataset[ORCIDItem] =spark.read.load(s"$workingPath/orcidworksWithAuthor").as[ORCIDItem] run(spark,workingPath, targetPath)
logger.info("Converting ORCID to OAF")
dataset.map(o => ORCIDToOAF.convertTOOAF(o)).write.mode(SaveMode.Overwrite).save(targetPath)
} }

2
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPreprocessORCID.scala
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@ -50,7 +50,7 @@ object SparkPreprocessORCID {
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
val conf: SparkConf = new SparkConf() val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_orcid_to_oaf_params.json"))) val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/preprocess_orcid_params.json")))
parser.parseArgument(args) parser.parseArgument(args)
val spark: SparkSession = val spark: SparkSession =
SparkSession SparkSession

101
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml
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@ -1,101 +0,0 @@
<workflow-app name="import Crossref from index into HDFS" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPath</name>
<description>the working dir base path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>timestamp</name>
<description>Timestamp for incremental Harvesting</description>
</property>
</parameters>
<start to="ImportCrossRef"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ImportCrossRef">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>
<arg>-t</arg><arg>${workingPath}/input/crossref/index_update</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-ts</arg><arg>${timestamp}</arg>
</java>
<ok to="GenerateDataset"/>
<error to="Kill"/>
</action>
<action name="GenerateDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ExtractCrossrefToOAF</name>
<class>eu.dnetlib.doiboost.crossref.CrossrefDataset</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--workingPath</arg><arg>/data/doiboost/input/crossref</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="RenameDataset"/>
<error to="Kill"/>
</action>
<action name="RenameDataset">
<fs>
<delete path='${workingPath}/input/crossref/crossref_ds'/>
<move source="${workingPath}/input/crossref/crossref_ds_updated"
target="${workingPath}/input/crossref/crossref_ds"/>
</fs>
<ok to="ConvertCrossrefToOAF"/>
<error to="Kill"/>
</action>
<action name="ConvertCrossrefToOAF">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ConvertCrossrefToOAF</name>
<class>eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingPath}/input/crossref/crossref_ds</arg>
<arg>--targetPath</arg><arg>${workingPath}/process/</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

38
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/config-default.xml
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@ -1,38 +0,0 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</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>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl: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>

96
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml
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@ -1,96 +0,0 @@
<workflow-app name="Create DOIBoostActionSet" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>hostedByMapPath</name>
<description>the Hosted By Map Path</description>
</property>
<property>
<name>affiliationPath</name>
<description>the Affliation Path</description>
</property>
<property>
<name>paperAffiliationPath</name>
<description>the paperAffiliation Path</description>
</property>
<property>
<name>workingDirPath</name>
<description>the Working Path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
</parameters>
<start to="CreateDOIBoost"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="CreateDOIBoost">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create DOIBoost Infospace</name>
<class>eu.dnetlib.doiboost.SparkGenerateDoiBoost</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
<arg>--affiliationPath</arg><arg>${affiliationPath}</arg>
<arg>--paperAffiliationPath</arg><arg>${paperAffiliationPath}</arg>
<arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="GenerateActionSet"/>
<error to="Kill"/>
</action>
<action name="GenerateActionSet">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Generate DOIBoost ActionSet</name>
<class>eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--dbPublicationPath</arg><arg>${workingDirPath}/doiBoostPublicationFiltered</arg>
<arg>--dbDatasetPath</arg><arg>${workingDirPath}/crossrefDataset</arg>
<arg>--crossRefRelation</arg><arg>${workingDirPath}/crossrefRelation</arg>
<arg>--dbaffiliationRelationPath</arg><arg>${workingDirPath}/doiBoostPublicationAffiliation</arg>
<arg>-do</arg><arg>${workingDirPath}/doiBoostOrganization</arg>
<arg>--targetPath</arg><arg>${workingDirPath}/actionDataSet</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

42
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/config-default.xml
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@ -1,42 +0,0 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</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.wf.rerun.failnodes</name>
<value>false</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl: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>

92
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml
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@ -1,92 +0,0 @@
<workflow-app name="import MAG into HDFS" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the working dir base path</description>
</property>
<property>
<name>targetPath</name>
<description>the working dir base path</description>
</property>
<property>
<name>workingPath</name>
<description>the working dir base path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</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}'/>
<mkdir path='${workingPath}'/>
</fs>
<ok to="ConvertMagToDataset"/>
<error to="Kill"/>
</action>
<action name="ConvertMagToDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert Mag to Dataset</name>
<class>eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="PreprocessMag"/>
<error to="Kill"/>
</action>
<action name="PreprocessMag">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert Mag to OAF Dataset</name>
<class>eu.dnetlib.doiboost.mag.SparkPreProcessMAG</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}/process</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

0
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/config-default.xml → dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/config-default.xml
View File

216
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml Normal file
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@ -0,0 +1,216 @@
<workflow-app name="Generate DOIBoost ActionSet" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<!-- Crossref Parameters -->
<property>
<name>inputPathCrossref</name>
<description>the Crossref input path</description>
</property>
<property>
<name>crossrefDumpPath</name>
<description>the Crossref dump path</description>
</property>
<!-- MAG Parameters -->
<property>
<name>MAGDumpPath</name>
<description>the MAG dump working path</description>
</property>
<property>
<name>inputPathMAG</name>
<description>the MAG working path</description>
</property>
<!-- ORCID Parameters -->
<property>
<name>inputPathOrcid</name>
<description>the ORCID input path</description>
</property>
<property>
<name>workingPathOrcid</name>
<description>the ORCID working path</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="resume_from"/>
<decision name="resume_from">
<switch>
<case to="UnpackCrossrefEntries">${wf:conf('resumeFrom') eq 'UnpackCrossrefEntries'}</case>
<case to="GenerateCrossrefDataset">${wf:conf('resumeFrom') eq 'GenerateCrossrefDataset'}</case>
<case to="ResetMagWorkingPath">${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'}</case>
<case to="ConvertMagToDataset">${wf:conf('resumeFrom') eq 'ConvertMagToDataset'}</case>
<case to="PreProcessORCID">${wf:conf('resumeFrom') eq 'PreProcessORCID'}</case>
<default to="ImportCrossRef"/>
</switch>
</decision>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ImportCrossRef">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords</main-class>
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
<arg>--crossrefFileNameTarGz</arg><arg>${crossrefDumpPath}/crossref.tar.gz</arg>
<arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
<arg>--outputPath</arg><arg>${crossrefDumpPath}/files/</arg>
</java>
<ok to="UnpackCrossrefEntries"/>
<error to="Kill"/>
</action>
<action name="UnpackCrossrefEntries">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>SparkUnpackCrossrefEntries</name>
<class>eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${crossrefDumpPath}/files</arg>
<arg>--targetPath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
</spark>
<ok to="GenerateCrossrefDataset"/>
<error to="Kill"/>
</action>
<action name="GenerateCrossrefDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>SparkGenerateCrossrefDataset</name>
<class>eu.dnetlib.doiboost.crossref.GenerateCrossrefDataset</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=7G
--executor-cores=2
--driver-memory=7G
--conf spark.sql.shuffle.partitions=3840
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
</spark>
<ok to="removeFiles"/>
<error to="Kill"/>
</action>
<action name="removeFiles">
<fs>
<!-- <delete path="${crossrefDumpPath}/files"/>-->
<delete path="${crossrefDumpPath}/crossref_unpack/"/>
</fs>
<ok to="ResetMagWorkingPath"/>
<error to="Kill"/>
</action>
<!-- MAG SECTION -->
<action name="ResetMagWorkingPath">
<fs>
<delete path="${inputPathMAG}/dataset"/>
<delete path="${inputPathMAG}/process"/>
</fs>
<ok to="ConvertMagToDataset"/>
<error to="Kill"/>
</action>
<action name="ConvertMagToDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert Mag to Dataset</name>
<class>eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${MAGDumpPath}</arg>
<arg>--targetPath</arg><arg>${inputPathMAG}/dataset</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="PreProcessORCID"/>
<error to="Kill"/>
</action>
<!-- ORCID SECTION -->
<action name="PreProcessORCID">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert ORCID to Dataset</name>
<class>eu.dnetlib.doiboost.orcid.SparkPreprocessORCID</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${inputPathOrcid}</arg>
<arg>--workingPath</arg><arg>${workingPathOrcid}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

0
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml → dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/config-default.xml
View File

206
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml → dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml
View File

@ -1,4 +1,4 @@
<workflow-app name="Generate DOIBoost ActionSet" xmlns="uri:oozie:workflow:0.5"> <workflow-app name="Generate DOIBoost ActionSet for PROD" xmlns="uri:oozie:workflow:0.5">
<parameters> <parameters>
<property> <property>
<name>sparkDriverMemory</name> <name>sparkDriverMemory</name>
@ -17,8 +17,6 @@
<name>sparkExecutorCores</name> <name>sparkExecutorCores</name>
<description>number of cores used by single executor</description> <description>number of cores used by single executor</description>
</property> </property>
<!-- Itersection Parameters --> <!-- Itersection Parameters -->
<property> <property>
<name>workingPath</name> <name>workingPath</name>
@ -40,29 +38,8 @@
<name>inputPathCrossref</name> <name>inputPathCrossref</name>
<description>the Crossref input path</description> <description>the Crossref input path</description>
</property> </property>
<property>
<name>crossrefDumpPath</name>
<description>the Crossref dump path</description>
</property>
<!-- <property>-->
<!-- <name>crossrefTimestamp</name>-->
<!-- <description>Timestamp for the Crossref incremental Harvesting</description>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>esServer</name>-->
<!-- <description>elasticsearch server url for the Crossref Harvesting</description>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>esIndex</name>-->
<!-- <description>elasticsearch index name for the Crossref Harvesting</description>-->
<!-- </property>-->
<!-- MAG Parameters --> <!-- MAG Parameters -->
<property>
<name>MAGDumpPath</name>
<description>the MAG dump working path</description>
</property>
<property> <property>
<name>inputPathMAG</name> <name>inputPathMAG</name>
<description>the MAG working path</description> <description>the MAG working path</description>
@ -76,11 +53,6 @@
</property> </property>
<!-- ORCID Parameters --> <!-- ORCID Parameters -->
<property>
<name>inputPathOrcid</name>
<description>the ORCID input path</description>
</property>
<property> <property>
<name>workingPathOrcid</name> <name>workingPathOrcid</name>
<description>the ORCID working path</description> <description>the ORCID working path</description>
@ -103,15 +75,12 @@
<decision name="resume_from"> <decision name="resume_from">
<switch> <switch>
<case to="ConvertCrossrefToOAF">${wf:conf('resumeFrom') eq 'ConvertCrossrefToOAF'}</case>
<case to="ResetMagWorkingPath">${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'}</case>
<case to="ProcessMAG">${wf:conf('resumeFrom') eq 'PreprocessMag'}</case> <case to="ProcessMAG">${wf:conf('resumeFrom') eq 'PreprocessMag'}</case>
<case to="ProcessUW">${wf:conf('resumeFrom') eq 'PreprocessUW'}</case> <case to="ProcessUW">${wf:conf('resumeFrom') eq 'PreprocessUW'}</case>
<case to="ProcessORCID">${wf:conf('resumeFrom') eq 'PreprocessORCID'}</case> <case to="ProcessORCID">${wf:conf('resumeFrom') eq 'ProcessORCID'}</case>
<case to="CreateDOIBoost">${wf:conf('resumeFrom') eq 'CreateDOIBoost'}</case> <case to="CreateDOIBoost">${wf:conf('resumeFrom') eq 'CreateDOIBoost'}</case>
<case to="GenerateActionSet">${wf:conf('resumeFrom') eq 'GenerateActionSet'}</case> <case to="GenerateActionSet">${wf:conf('resumeFrom') eq 'GenerateActionSet'}</case>
<case to="GenerateCrossrefDataset">${wf:conf('resumeFrom') eq 'GenerateCrossrefDataset'}</case> <default to="ConvertCrossrefToOAF"/>
<default to="ImportCrossRef"/>
</switch> </switch>
</decision> </decision>
@ -119,170 +88,6 @@
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message> <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill> </kill>
<!-- <action name="ImportCrossRef">-->
<!-- <java>-->
<!-- <main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>-->
<!-- <arg>&#45;&#45;targetPath</arg><arg>${inputPathCrossref}/index_update</arg>-->
<!-- <arg>&#45;&#45;namenode</arg><arg>${nameNode}</arg>-->
<!-- <arg>&#45;&#45;esServer</arg><arg>${esServer}</arg>-->
<!-- <arg>&#45;&#45;esIndex</arg><arg>${esIndex}</arg>-->
<!-- <arg>&#45;&#45;timestamp</arg><arg>${crossrefTimestamp}</arg>-->
<!-- </java>-->
<!-- <ok to="GenerateCrossrefDataset"/>-->
<!-- <error to="Kill"/>-->
<!-- </action>-->
<action name="ImportCrossRef">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords</main-class>
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
<arg>--crossrefFileNameTarGz</arg><arg>${crossrefDumpPath}/crossref.tar.gz</arg>
<arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
<arg>--outputPath</arg><arg>${crossrefDumpPath}/files/</arg>
</java>
<ok to="UnpackCrossrefEntries"/>
<error to="Kill"/>
</action>
<action name="UnpackCrossrefEntries">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>SparkUnpackCrossrefEntries</name>
<class>eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${crossrefDumpPath}/files</arg>
<arg>--targetPath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
</spark>
<ok to="GenerateCrossrefDataset"/>
<error to="Kill"/>
</action>
<action name="GenerateCrossrefDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>SparkGenerateCrossrefDataset</name>
<class>eu.dnetlib.doiboost.crossref.GenerateCrossrefDataset</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=7G
--executor-cores=2
--driver-memory=7G
--conf spark.sql.shuffle.partitions=3840
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
</spark>
<ok to="removeFiles"/>
<error to="Kill"/>
</action>
<action name="removeFiles">
<fs>
<!-- <delete path="${crossrefDumpPath}/files"/>-->
<delete path="${crossrefDumpPath}/crossref_unpack/"/>
</fs>
<ok to="ResetMagWorkingPath"/>
<error to="Kill"/>
</action>
<!-- CROSSREF SECTION -->
<!-- <action name="GenerateCrossrefDataset">-->
<!-- <spark xmlns="uri:oozie:spark-action:0.2">-->
<!-- <master>yarn-cluster</master>-->
<!-- <mode>cluster</mode>-->
<!-- <name>GenerateCrossrefDataset</name>-->
<!-- <class>eu.dnetlib.doiboost.crossref.CrossrefDataset</class>-->
<!-- <jar>dhp-doiboost-${projectVersion}.jar</jar>-->
<!-- <spark-opts>-->
<!-- &#45;&#45;executor-memory=${sparkExecutorMemory}-->
<!-- &#45;&#45;executor-cores=${sparkExecutorCores}-->
<!-- &#45;&#45;driver-memory=${sparkDriverMemory}-->
<!-- &#45;&#45;conf spark.sql.shuffle.partitions=3840-->
<!-- &#45;&#45;conf spark.extraListeners=${spark2ExtraListeners}-->
<!-- &#45;&#45;conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}-->
<!-- &#45;&#45;conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}-->
<!-- &#45;&#45;conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}-->
<!-- </spark-opts>-->
<!-- <arg>&#45;&#45;workingPath</arg><arg>${inputPathCrossref}</arg>-->
<!-- <arg>&#45;&#45;master</arg><arg>yarn-cluster</arg>-->
<!-- </spark>-->
<!-- <ok to="RenameDataset"/>-->
<!-- <error to="Kill"/>-->
<!-- </action>-->
<!-- <action name="RenameDataset">-->
<!-- <fs>-->
<!-- <delete path="${inputPathCrossref}/crossref_ds"/>-->
<!-- <move source="${inputPathCrossref}/crossref_ds_updated"-->
<!-- target="${inputPathCrossref}/crossref_ds"/>-->
<!-- </fs>-->
<!-- <ok to="ResetMagWorkingPath"/>-->
<!-- <error to="Kill"/>-->
<!-- </action>-->
<!-- MAG SECTION -->
<action name="ResetMagWorkingPath">
<fs>
<delete path="${inputPathMAG}/dataset"/>
<delete path="${inputPathMAG}/process"/>
</fs>
<ok to="ConvertMagToDataset"/>
<error to="Kill"/>
</action>
<action name="ConvertMagToDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert Mag to Dataset</name>
<class>eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${MAGDumpPath}</arg>
<arg>--targetPath</arg><arg>${inputPathMAG}/dataset</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="ConvertCrossrefToOAF"/>
<error to="Kill"/>
</action>
<action name="ConvertCrossrefToOAF"> <action name="ConvertCrossrefToOAF">
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master> <master>yarn-cluster</master>
@ -326,7 +131,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${inputPathMAG}/dataset</arg> <arg>--sourcePath</arg><arg>${inputPathMAG}/dataset</arg>
<arg>--workingPath</arg><arg>${inputPathMAG}/process</arg> <arg>--workingPath</arg><arg>${inputPathMAG}/process_p</arg>
<arg>--targetPath</arg><arg>${workingPath}</arg> <arg>--targetPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg> <arg>--master</arg><arg>yarn-cluster</arg>
</spark> </spark>
@ -368,7 +173,7 @@
<master>yarn-cluster</master> <master>yarn-cluster</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Convert ORCID to Dataset</name> <name>Convert ORCID to Dataset</name>
<class>eu.dnetlib.doiboost.orcid.SparkPreprocessORCID</class> <class>eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar> <jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
@ -380,7 +185,6 @@
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${inputPathOrcid}</arg>
<arg>--workingPath</arg><arg>${workingPathOrcid}</arg> <arg>--workingPath</arg><arg>${workingPathOrcid}</arg>
<arg>--targetPath</arg><arg>${workingPath}/orcidPublication</arg> <arg>--targetPath</arg><arg>${workingPath}/orcidPublication</arg>
<arg>--master</arg><arg>yarn-cluster</arg> <arg>--master</arg><arg>yarn-cluster</arg>

38
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/config-default.xml
View File

@ -1,38 +0,0 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</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>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl: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>

55
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/workflow.xml
View File

@ -1,55 +0,0 @@
<workflow-app name="import UnpayWall into HDFS" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the working dir base path</description>
</property>
<property>
<name>targetPath</name>
<description>the working dir base path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
</parameters>
<start to="PreprocessUW"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="PreprocessUW">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert UnpayWall to Dataset</name>
<class>eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/uw_extracted</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

49
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala
View File

@ -1,22 +1,15 @@
package eu.dnetlib.doiboost.mag package eu.dnetlib.doiboost.mag
import java.sql.Timestamp import org.apache.spark.SparkConf
import org.apache.spark.sql.{Dataset, SparkSession}
import eu.dnetlib.dhp.schema.oaf.Publication import org.codehaus.jackson.map.ObjectMapper
import org.apache.htrace.fasterxml.jackson.databind.SerializationFeature
import org.apache.spark.{SparkConf, SparkContext}
import org.apache.spark.api.java.function.MapFunction
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.junit.jupiter.api.Test
import org.slf4j.{Logger, LoggerFactory}
import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.Assertions._
import org.apache.spark.sql.functions._ import org.junit.jupiter.api.Test
import org.json4s.DefaultFormats
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._ import java.sql.Timestamp
import scala.io.Source import scala.io.Source
import scala.reflect.ClassTag
import scala.util.matching.Regex
@ -65,14 +58,19 @@ class MAGMappingTest {
@Test @Test
def normalizeDoiTest():Unit = { def normalizeDoiTest():Unit = {
import org.json4s.jackson.Serialization.write
import org.json4s.DefaultFormats
implicit val formats = DefaultFormats implicit val formats = DefaultFormats
val conf = new SparkConf().setAppName("test").setMaster("local[2]") val conf = new SparkConf()
val sc = new SparkContext(conf) conf.setMaster("local[*]")
val spark = SparkSession.builder.config(sc.getConf).getOrCreate() conf.set("spark.driver.host", "localhost")
val spark: SparkSession =
SparkSession
.builder()
.appName(getClass.getSimpleName)
.config(conf)
.getOrCreate()
val path = getClass.getResource("magPapers.json").getPath val path = getClass.getResource("magPapers.json").getPath
import org.apache.spark.sql.Encoders import org.apache.spark.sql.Encoders
@ -90,14 +88,19 @@ class MAGMappingTest {
@Test @Test
def normalizeDoiTest2():Unit = { def normalizeDoiTest2():Unit = {
import org.json4s.jackson.Serialization.write
import org.json4s.DefaultFormats import org.json4s.DefaultFormats
implicit val formats = DefaultFormats implicit val formats = DefaultFormats
val conf = new SparkConf().setAppName("test").setMaster("local[2]") val conf = new SparkConf()
val sc = new SparkContext(conf) conf.setMaster("local[*]")
val spark = SparkSession.builder.config(sc.getConf).getOrCreate() conf.set("spark.driver.host", "localhost")
val spark: SparkSession =
SparkSession
.builder()
.appName(getClass.getSimpleName)
.config(conf)
.getOrCreate()
val path = getClass.getResource("duplicatedMagPapers.json").getPath val path = getClass.getResource("duplicatedMagPapers.json").getPath
import org.apache.spark.sql.Encoders import org.apache.spark.sql.Encoders

6
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala
View File

@ -48,6 +48,8 @@ class MappingORCIDToOAFTest {
SparkPreprocessORCID.run( spark,sourcePath, workingPath) SparkPreprocessORCID.run( spark,sourcePath, workingPath)
SparkConvertORCIDToOAF.run(spark, workingPath,targetPath)
val mapper = new ObjectMapper() val mapper = new ObjectMapper()
@ -61,6 +63,8 @@ class MappingORCIDToOAFTest {
assertTrue(oA == p.count()) assertTrue(oA == p.count())
println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(p.first())) println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(p.first()))
spark.close()
} }
@ -78,7 +82,7 @@ class MappingORCIDToOAFTest {
val oaf = ORCIDToOAF.convertTOOAF(orcid) val oaf = ORCIDToOAF.convertTOOAF(orcid)
assert(oaf.getPid.size() == 1) assert(oaf.getPid.size() == 1)
oaf.getPid.toList.foreach(pid => assert(pid.getQualifier.getClassid.equals("doi"))) oaf.getPid.toList.foreach(pid => assert(pid.getQualifier.getClassid.equals("doi")))
oaf.getPid.toList.foreach(pid => assert(pid.getValue.equals("10.1042/BCJ20160876".toLowerCase()))) oaf.getPid.toList.foreach(pid => assert(pid.getValue.equals("10.1042/BCJ20160876")))
//println(mapper.writeValueAsString(ORCIDToOAF.convertTOOAF(orcid))) //println(mapper.writeValueAsString(ORCIDToOAF.convertTOOAF(orcid)))