renamed wrong package, implemented last aggregation workflow for scholexplorer
parent
51a03c0a50
commit
7b15b88d4c
@ -1,4 +1,4 @@
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package eu.dnetllib.dhp.sx.bio
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package eu.dnetlib.dhp.sx.bio
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import eu.dnetlib.dhp.schema.common.ModelConstants
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import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, OafMapperUtils}
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@ -1,10 +1,10 @@
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package eu.dnetllib.dhp.sx.bio.ebi
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package eu.dnetlib.dhp.sx.bio.ebi
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
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import eu.dnetlib.dhp.schema.oaf.Result
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import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
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import eu.dnetlib.dhp.utils.ISLookupClientFactory
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import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
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import org.apache.commons.io.IOUtils
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import org.apache.hadoop.conf.Configuration
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import org.apache.hadoop.fs.{FSDataOutputStream, FileSystem, Path}
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@ -1,8 +1,9 @@
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package eu.dnetllib.dhp.sx.bio.ebi
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package eu.dnetlib.dhp.sx.bio.ebi
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetllib.dhp.sx.bio.BioDBToOAF.EBILinkItem
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import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
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import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
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import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
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import eu.dnetlib.dhp.sx.bio.pubmed.PMJournal
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import org.apache.commons.io.IOUtils
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import org.apache.http.client.config.RequestConfig
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import org.apache.http.client.methods.HttpGet
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@ -1,9 +1,10 @@
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package eu.dnetllib.dhp.sx.bio.ebi
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package eu.dnetlib.dhp.sx.bio.ebi
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.oaf.Oaf
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import eu.dnetllib.dhp.sx.bio.BioDBToOAF
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import eu.dnetllib.dhp.sx.bio.BioDBToOAF.EBILinkItem
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import eu.dnetlib.dhp.sx.bio.BioDBToOAF
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import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
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import BioDBToOAF.EBILinkItem
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import org.apache.commons.io.IOUtils
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import org.apache.spark.SparkConf
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import org.apache.spark.sql._
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@ -1,5 +1,5 @@
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package eu.dnetllib.dhp.sx.bio.pubmed;
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package eu.dnetlib.dhp.sx.bio.pubmed;
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import java.io.Serializable;
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import java.util.ArrayList;
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@ -1,5 +1,5 @@
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package eu.dnetllib.dhp.sx.bio.pubmed;
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package eu.dnetlib.dhp.sx.bio.pubmed;
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import java.io.Serializable;
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package eu.dnetllib.dhp.sx.bio.pubmed;
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package eu.dnetlib.dhp.sx.bio.pubmed;
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public class PMGrant {
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package eu.dnetllib.dhp.sx.bio.pubmed;
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package eu.dnetlib.dhp.sx.bio.pubmed;
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import java.io.Serializable;
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@ -1,4 +1,4 @@
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package eu.dnetllib.dhp.sx.bio.pubmed
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package eu.dnetlib.dhp.sx.bio.pubmed
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import scala.xml.MetaData
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import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
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@ -1,5 +1,5 @@
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package eu.dnetllib.dhp.sx.bio.pubmed;
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package eu.dnetlib.dhp.sx.bio.pubmed;
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public class PMSubject {
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private String value;
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@ -1,4 +1,4 @@
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package eu.dnetllib.dhp.sx.bio.pubmed
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package eu.dnetlib.dhp.sx.bio.pubmed
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
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import eu.dnetlib.dhp.schema.common.ModelConstants
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@ -0,0 +1,51 @@
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<workflow-app name="Transform_BioEntity_Workflow" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sourcePath</name>
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<description>the PDB Database Working Path</description>
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</property>
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<property>
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<name>database</name>
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<description>the PDB Database Working Path</description>
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</property>
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<property>
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<name>targetPath</name>
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<description>the Target Working dir path</description>
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</property>
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</parameters>
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<start to="ConvertDB"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ConvertDB">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Convert Bio DB to OAF Dataset</name>
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<class>eu.dnetlib.dhp.sx.bio.SparkTransformBioDatabaseToOAF</class>
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<jar>dhp-aggregation-${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.shuffle.partitions=2000
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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>--master</arg><arg>yarn</arg>
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<arg>--dbPath</arg><arg>${sourcePath}</arg>
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<arg>--database</arg><arg>${database}</arg>
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<arg>--targetPath</arg><arg>${targetPath}</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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@ -1,10 +1,10 @@
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package eu.dnetllib.dhp.sx.bio
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package eu.dnetlib.dhp.sx.bio
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import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature}
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import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
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import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
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import eu.dnetllib.dhp.sx.bio.BioDBToOAF.ScholixResolved
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import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf}
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import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
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import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf}
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import org.json4s.DefaultFormats
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import org.json4s.JsonAST.{JField, JObject, JString}
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import org.json4s.jackson.JsonMethods.parse
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@ -1,177 +0,0 @@
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<workflow-app name="Transform_BioEntity_Workflow" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>PDBPath</name>
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<description>the PDB Database Working Path</description>
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</property>
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<property>
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<name>UNIPROTDBPath</name>
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<description>the UNIPROT Database Working Path</description>
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</property>
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<property>
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<name>EBIDataset</name>
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<description>the EBI Links Dataset Path</description>
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</property>
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<property>
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<name>ScholixResolvedDBPath</name>
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<description>the Scholix Resolved Dataset Path</description>
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</property>
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<property>
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<name>CrossrefLinksPath</name>
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<description>the CrossrefLinks Path</description>
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</property>
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<property>
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<name>targetPath</name>
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<description>the Target Working dir path</description>
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</property>
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</parameters>
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<start to="ConvertPDB"/>
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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="ConvertPDB">
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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 PDB to OAF Dataset</name>
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<class>eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF</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=${spark2ExtraListeners}
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--conf spark.sql.shuffle.partitions=2000
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--master</arg><arg>yarn</arg>
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<arg>--dbPath</arg><arg>${PDBPath}</arg>
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<arg>--database</arg><arg>PDB</arg>
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<arg>--targetPath</arg><arg>${targetPath}/pdb_OAF</arg>
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</spark>
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<ok to="ConvertUNIPROT"/>
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<error to="Kill"/>
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</action>
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<action name="ConvertUNIPROT">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Convert UNIPROT to OAF Dataset</name>
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<class>eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF</class>
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<jar>dhp-graph-mapper-${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.shuffle.partitions=2000
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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>--master</arg><arg>yarn</arg>
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<arg>--dbPath</arg><arg>${UNIPROTDBPath}</arg>
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<arg>--database</arg><arg>UNIPROT</arg>
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<arg>--targetPath</arg><arg>${targetPath}/uniprot_OAF</arg>
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</spark>
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<ok to="ConvertEBILinks"/>
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<error to="Kill"/>
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</action>
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<action name="ConvertEBILinks">
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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 EBI Links to OAF Dataset</name>
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<class>eu.dnetlib.dhp.sx.graph.ebi.SparkEBILinksToOaf</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=${spark2ExtraListeners}
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--conf spark.sql.shuffle.partitions=2000
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--master</arg><arg>yarn</arg>
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<arg>--sourcePath</arg><arg>${EBIDataset}</arg>
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<arg>--targetPath</arg><arg>${targetPath}/ebi_OAF</arg>
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</spark>
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<ok to="ConvertScholixResolved"/>
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<error to="Kill"/>
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</action>
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<action name="ConvertScholixResolved">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Convert Scholix to OAF Dataset</name>
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<class>eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF</class>
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<jar>dhp-graph-mapper-${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.shuffle.partitions=2000
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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>--master</arg><arg>yarn</arg>
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<arg>--dbPath</arg><arg>${ScholixResolvedDBPath}</arg>
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<arg>--database</arg><arg>SCHOLIX</arg>
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<arg>--targetPath</arg><arg>${targetPath}/scholix_resolved_OAF</arg>
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</spark>
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<ok to="ConvertCrossrefLinks"/>
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<error to="Kill"/>
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</action>
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<action name="ConvertCrossrefLinks">
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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 Crossref Links to OAF Dataset</name>
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<class>eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF</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=${spark2ExtraListeners}
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--conf spark.sql.shuffle.partitions=2000
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--master</arg><arg>yarn</arg>
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<arg>--dbPath</arg><arg>${CrossrefLinksPath}</arg>
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<arg>--database</arg><arg>CROSSREF_LINKS</arg>
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<arg>--targetPath</arg><arg>${targetPath}/crossref_unresolved_relation_OAF</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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