updated pubmed
parent
c00be646f3
commit
714b71bd21
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package eu.dnetlib.dhp.sx.ebi.model;
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public class PMGrant {
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private String grantID;
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private String agency;
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private String country;
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public PMGrant() {
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}
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public PMGrant(String grantID, String agency, String country) {
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this.grantID = grantID;
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this.agency = agency;
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this.country = country;
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}
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public String getGrantID() {
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return grantID;
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}
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public void setGrantID(String grantID) {
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this.grantID = grantID;
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}
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public String getAgency() {
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return agency;
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}
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public void setAgency(String agency) {
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this.agency = agency;
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}
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public String getCountry() {
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return country;
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}
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public void setCountry(String country) {
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this.country = country;
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}
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}
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@ -0,0 +1,41 @@
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package eu.dnetlib.dhp.sx.ebi.model;
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public class PMSubject {
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private String value;
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private String meshId;
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private String registryNumber;
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public PMSubject() {
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}
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public PMSubject(String value, String meshId, String registryNumber) {
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this.value = value;
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this.meshId = meshId;
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this.registryNumber = registryNumber;
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}
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public String getValue() {
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return value;
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}
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public void setValue(String value) {
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this.value = value;
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}
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public String getMeshId() {
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return meshId;
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}
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public void setMeshId(String meshId) {
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this.meshId = meshId;
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}
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public String getRegistryNumber() {
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return registryNumber;
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}
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public void setRegistryNumber(String registryNumber) {
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this.registryNumber = registryNumber;
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}
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}
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@ -0,0 +1,19 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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</configuration>
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<workflow-app name="Transform_Pubmed_Workflow" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>baselineWorkingPath</name>
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<description>the Baseline Working Path</description>
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</property>
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</parameters>
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<start to="ConvertDataset"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ConvertDataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Convert Baseline to Dataset</name>
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<class>eu.dnetlib.dhp.sx.ebi.SparkCreateBaselineDataFrame</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--workingPath</arg><arg>${baselineWorkingPath}</arg>
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<arg>--master</arg><arg>yarn</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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@ -0,0 +1,4 @@
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[
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{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
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{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true}
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]
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