PDBPath
the PDB Database Working Path
UNIPROTDBPath
the UNIPROT Database Working Path
EBIDataset
the EBI Links Dataset Path
targetPath
the Target Working dir path
Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]
yarn
cluster
Convert PDB to OAF Dataset
eu.dnetlib.dhp.sx.bio.SparkTransformBioDatabaseToOAF
dhp-graph-mapper-${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.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${targetPath}/uniprot_OAF
yarn
cluster
Convert EBI Links to OAF Dataset
eu.dnetlib.dhp.sx.ebi.SparkEBILinksToOaf
dhp-graph-mapper-${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