PDBPath
the PDB Database Working Path
UNIPROTDBPath
the UNIPROT Database Working Path
EBIDataset
the EBI Links Dataset Path
ScholixResolvedDBPath
the Scholix Resolved Dataset Path
CrossrefLinksPath
the CrossrefLinks Path
targetPath
the Target Working dir path
Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]
yarn
cluster
Convert PDB to OAF Dataset
eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF
dhp-graph-mapper-${projectVersion}.jar
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=2000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--masteryarn
--dbPath${PDBPath}
--databasePDB
--targetPath${targetPath}/pdb_OAF
yarn
cluster
Convert UNIPROT to OAF Dataset
eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF
dhp-graph-mapper-${projectVersion}.jar
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=2000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--masteryarn
--dbPath${UNIPROTDBPath}
--databaseUNIPROT
--targetPath${targetPath}/uniprot_OAF
yarn
cluster
Convert EBI Links to OAF Dataset
eu.dnetlib.dhp.sx.graph.ebi.SparkEBILinksToOaf
dhp-graph-mapper-${projectVersion}.jar
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=2000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--masteryarn
--sourcePath${EBIDataset}
--targetPath${targetPath}/ebi_OAF
yarn
cluster
Convert Scholix to OAF Dataset
eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF
dhp-graph-mapper-${projectVersion}.jar
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=2000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--masteryarn
--dbPath${ScholixResolvedDBPath}
--databaseSCHOLIX
--targetPath${targetPath}/scholix_resolved_OAF
yarn
cluster
Convert Crossref Links to OAF Dataset
eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF
dhp-graph-mapper-${projectVersion}.jar
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.shuffle.partitions=2000
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--masteryarn
--dbPath${CrossrefLinksPath}
--databaseCROSSREF_LINKS
--targetPath${targetPath}/crossref_unresolved_relation_OAF