forked from D-Net/dnet-hadoop
64 lines
2.3 KiB
Scala
64 lines
2.3 KiB
Scala
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.collection.CollectionUtils
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import eu.dnetlib.dhp.schema.oaf.Oaf
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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 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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import org.slf4j.{Logger, LoggerFactory}
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import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH}
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import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion
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import eu.dnetlib.dhp.utils.DHPUtils.{MAPPER, writeHdfsFile}
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object SparkEBILinksToOaf {
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def main(args: Array[String]): Unit = {
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val log: Logger = LoggerFactory.getLogger(getClass)
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val conf: SparkConf = new SparkConf()
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val parser = new ArgumentApplicationParser(
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IOUtils.toString(
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getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/ebi_to_df_params.json")
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)
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)
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parser.parseArgument(args)
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val spark: SparkSession =
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SparkSession
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.builder()
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.config(conf)
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.appName(SparkEBILinksToOaf.getClass.getSimpleName)
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.master(parser.get("master"))
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.getOrCreate()
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import spark.implicits._
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val sourcePath = parser.get("sourcePath")
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log.info(s"sourcePath -> $sourcePath")
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val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
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log.info("mdstoreOutputVersion: {}", mdstoreOutputVersion)
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val cleanedMdStoreVersion = MAPPER.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
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val outputBasePath = cleanedMdStoreVersion.getHdfsPath
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log.info("outputBasePath: {}", outputBasePath)
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implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
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val ebLinks: Dataset[EBILinkItem] = spark.read
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.load(sourcePath)
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.as[EBILinkItem]
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.filter(l => l.links != null && l.links.startsWith("{"))
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CollectionUtils.saveDataset(
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ebLinks
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.flatMap(j => BioDBToOAF.parse_ebi_links(j.links))
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.filter(p => BioDBToOAF.EBITargetLinksFilter(p))
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.flatMap(p => BioDBToOAF.convertEBILinksToOaf(p)),
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s"$outputBasePath/$MDSTORE_DATA_PATH"
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)
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val df = spark.read.text(s"$outputBasePath/$MDSTORE_DATA_PATH")
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val mdStoreSize = df.count
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writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$mdStoreSize", s"$outputBasePath/$MDSTORE_SIZE_PATH")
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}
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}
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