79 lines
2.9 KiB
Scala
79 lines
2.9 KiB
Scala
package eu.dnetlib.dhp.sx.bio
|
|
|
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
|
import eu.dnetlib.dhp.collection.CollectionUtils
|
|
import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH}
|
|
import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion
|
|
import eu.dnetlib.dhp.schema.oaf.Oaf
|
|
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
|
|
import org.apache.commons.io.IOUtils
|
|
import org.apache.spark.SparkConf
|
|
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
|
|
import org.slf4j.{Logger, LoggerFactory}
|
|
import eu.dnetlib.dhp.utils.DHPUtils.{MAPPER, writeHdfsFile}
|
|
|
|
object SparkTransformBioDatabaseToOAF {
|
|
|
|
def main(args: Array[String]): Unit = {
|
|
val conf: SparkConf = new SparkConf()
|
|
val log: Logger = LoggerFactory.getLogger(getClass)
|
|
val parser = new ArgumentApplicationParser(
|
|
IOUtils.toString(
|
|
getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json")
|
|
)
|
|
)
|
|
parser.parseArgument(args)
|
|
val database: String = parser.get("database")
|
|
log.info("database: {}", database)
|
|
|
|
val dbPath: String = parser.get("dbPath")
|
|
log.info("dbPath: {}", database)
|
|
|
|
val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
|
|
log.info("mdstoreOutputVersion: {}", mdstoreOutputVersion)
|
|
|
|
val cleanedMdStoreVersion = MAPPER.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
|
|
val outputBasePath = cleanedMdStoreVersion.getHdfsPath
|
|
log.info("outputBasePath: {}", outputBasePath)
|
|
|
|
val spark: SparkSession =
|
|
SparkSession
|
|
.builder()
|
|
.config(conf)
|
|
.appName(getClass.getSimpleName)
|
|
.master(parser.get("master"))
|
|
.getOrCreate()
|
|
val sc = spark.sparkContext
|
|
|
|
implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
|
|
import spark.implicits._
|
|
database.toUpperCase() match {
|
|
case "UNIPROT" =>
|
|
CollectionUtils.saveDataset(
|
|
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))),
|
|
s"$outputBasePath/$MDSTORE_DATA_PATH"
|
|
)
|
|
case "PDB" =>
|
|
CollectionUtils.saveDataset(
|
|
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))),
|
|
s"$outputBasePath/$MDSTORE_DATA_PATH"
|
|
)
|
|
case "SCHOLIX" =>
|
|
CollectionUtils.saveDataset(
|
|
spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)),
|
|
s"$outputBasePath/$MDSTORE_DATA_PATH"
|
|
)
|
|
case "CROSSREF_LINKS" =>
|
|
CollectionUtils.saveDataset(
|
|
spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))),
|
|
s"$outputBasePath/$MDSTORE_DATA_PATH"
|
|
)
|
|
}
|
|
|
|
val df = spark.read.text(s"$outputBasePath/$MDSTORE_DATA_PATH")
|
|
val mdStoreSize = df.count
|
|
writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$mdStoreSize", s"$outputBasePath/$MDSTORE_SIZE_PATH")
|
|
}
|
|
|
|
}
|