From 2557bb41f54cbe8232372bfa1c554ce5d3177cbd Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 6 Oct 2021 16:41:08 +0200 Subject: [PATCH] Implemented new method for update baseline inside scala node --- .../ebi/SparkCreateBaselineDataFrame.scala | 123 +- .../sx/graph/ebi/SparkDownloadEBILinks.scala | 45 +- .../sx/graph/ebi/baseline_to_oaf_params.json | 9 +- .../dhp/sx/graph/ebi/ebi_download_update.json | 6 +- .../dhp/sx/graph/ebi/oozie_app/workflow.xml | 2 +- .../graph/ebi/update/oozie_app/workflow.xml | 116 +- .../sx/graph/bio/pubmed/BioScholixTest.scala | 7 +- .../dnetlib/dhp/sx/graph/bio/pubmed/ls_result | 1433 +++++++++++++++++ 8 files changed, 1625 insertions(+), 116 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/ls_result diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkCreateBaselineDataFrame.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkCreateBaselineDataFrame.scala index 26efd723f..ee76cf8ad 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkCreateBaselineDataFrame.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkCreateBaselineDataFrame.scala @@ -6,18 +6,130 @@ import eu.dnetlib.dhp.schema.oaf.Result import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf} import eu.dnetlib.dhp.utils.ISLookupClientFactory import org.apache.commons.io.IOUtils +import org.apache.hadoop.conf.Configuration +import org.apache.hadoop.fs.{FSDataOutputStream, FileSystem, Path} +import org.apache.http.client.config.RequestConfig +import org.apache.http.client.methods.HttpGet +import org.apache.http.impl.client.HttpClientBuilder import org.apache.spark.SparkConf import org.apache.spark.rdd.RDD import org.apache.spark.sql.expressions.Aggregator import org.apache.spark.sql._ import org.slf4j.{Logger, LoggerFactory} +import java.io.InputStream import scala.io.Source import scala.xml.pull.XMLEventReader object SparkCreateBaselineDataFrame { + def requestBaseLineUpdatePage(maxFile:String):List[(String,String)] = { + val data =requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/") + + val result =data.lines.filter(l => l.startsWith("") + val start = l.indexOf("= 0 && end >start) + l.substring(start+9, (end-start)) + else + "" + }.filter(s =>s.endsWith(".gz") ).filter(s => s > maxFile).map(s => (s,s"https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/$s")).toList + + result + } + + + def downloadBaselinePart(url:String):InputStream = { + val r = new HttpGet(url) + val timeout = 60; // seconds + val config = RequestConfig.custom() + .setConnectTimeout(timeout * 1000) + .setConnectionRequestTimeout(timeout * 1000) + .setSocketTimeout(timeout * 1000).build() + val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build() + val response = client.execute(r) + println(s"get response with status${response.getStatusLine.getStatusCode}") + response.getEntity.getContent + + } + + def requestPage(url:String):String = { + val r = new HttpGet(url) + val timeout = 60; // seconds + val config = RequestConfig.custom() + .setConnectTimeout(timeout * 1000) + .setConnectionRequestTimeout(timeout * 1000) + .setSocketTimeout(timeout * 1000).build() + val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build() + try { + var tries = 4 + while (tries > 0) { + println(s"requesting ${r.getURI}") + try { + val response = client.execute(r) + println(s"get response with status${response.getStatusLine.getStatusCode}") + if (response.getStatusLine.getStatusCode > 400) { + tries -= 1 + } + else + return IOUtils.toString(response.getEntity.getContent) + } catch { + case e: Throwable => + println(s"Error on requesting ${r.getURI}") + e.printStackTrace() + tries -= 1 + } + } + "" + } finally { + if (client != null) + client.close() + } + } + + + + + + + def downloadBaseLineUpdate(baselinePath:String, hdfsServerUri:String ):Unit = { + + + val conf = new Configuration + conf.set("fs.defaultFS", hdfsServerUri) + val fs = FileSystem.get(conf) + val p = new Path(baselinePath) + val files = fs.listFiles(p,false) + var max_file = "" + while (files.hasNext) { + val c = files.next() + val data = c.getPath.toString + val fileName = data.substring(data.lastIndexOf("/")+1) + + if (fileName> max_file) + max_file = fileName + } + + val files_to_download = requestBaseLineUpdatePage(max_file) + + files_to_download.foreach { u => + val hdfsWritePath: Path = new Path(s"$baselinePath/${u._1}") + val fsDataOutputStream: FSDataOutputStream = fs.create(hdfsWritePath, true) + val i = downloadBaselinePart(u._2) + val buffer = Array.fill[Byte](1024)(0) + while(i.read(buffer)>0) { + fsDataOutputStream.write(buffer) + } + i.close() + println(s"Downloaded ${u._2} into $baselinePath/${u._1}") + fsDataOutputStream.close() + } + + } + + val pmArticleAggregator: Aggregator[(String, PMArticle), PMArticle, PMArticle] = new Aggregator[(String, PMArticle), PMArticle, PMArticle] with Serializable { override def zero: PMArticle = new PMArticle @@ -51,6 +163,10 @@ object SparkCreateBaselineDataFrame { val targetPath = parser.get("targetPath") log.info("targetPath: {}", targetPath) + val hdfsServerUri = parser.get("hdfsServerUri") + log.info("hdfsServerUri: {}", targetPath) + + val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl) val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService) val spark: SparkSession = @@ -61,16 +177,15 @@ object SparkCreateBaselineDataFrame { .master(parser.get("master")).getOrCreate() import spark.implicits._ - val sc = spark.sparkContext - - implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle]) implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal]) implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor]) implicit val resultEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) + downloadBaseLineUpdate(s"$workingPath/baseline", hdfsServerUri) + val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline",2000) val ds:Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i =>{ val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes())) @@ -87,7 +202,5 @@ object SparkCreateBaselineDataFrame { .map(a => PubMedToOaf.convert(a, vocabularies)).as[Result] .filter(p => p!= null) .write.mode(SaveMode.Overwrite).save(targetPath) - - //s"$workingPath/oaf/baseline_oaf" } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkDownloadEBILinks.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkDownloadEBILinks.scala index eda825bd0..e940fdff0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkDownloadEBILinks.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkDownloadEBILinks.scala @@ -4,20 +4,16 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.EBILinkItem import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal} import org.apache.commons.io.IOUtils -import org.apache.hadoop.conf.Configuration -import org.apache.hadoop.fs.{FileSystem, Path} import org.apache.http.client.config.RequestConfig -import org.apache.http.client.methods.{HttpGet, HttpUriRequest} +import org.apache.http.client.methods.HttpGet import org.apache.http.impl.client.HttpClientBuilder import org.apache.spark.SparkConf -import org.apache.spark.sql.expressions.Aggregator import org.apache.spark.sql.functions.max -import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.apache.spark.sql._ import org.slf4j.{Logger, LoggerFactory} object SparkDownloadEBILinks { - def createEBILinks(pmid:Long):EBILinkItem = { val res = requestLinks(pmid) @@ -26,7 +22,6 @@ object SparkDownloadEBILinks { null } - def requestPage(url:String):String = { val r = new HttpGet(url) val timeout = 60; // seconds @@ -61,42 +56,6 @@ object SparkDownloadEBILinks { } } - - def requestBaseLineUpdatePage():List[String] = { - val data =requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/") - - val result =data.lines.filter(l => l.startsWith("") - val start = l.indexOf("= 0 && end >start) - l.substring(start+9, (end-start)) - else - "" - }.filter(s =>s.endsWith(".gz") ).map(s => s"https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/$s").toList - - result - } - - def downloadBaseLineUpdate(baselinePath:String, hdfsServerUri:String ):Unit = { - - - val conf = new Configuration - conf.set("fs.defaultFS", hdfsServerUri) - val fs = FileSystem.get(conf) - val p = new Path((baselinePath)) - val files = fs.listFiles(p,false) - - while (files.hasNext) { - val c = files.next() - c.getPath - - } - - - } - - def requestLinks(PMID:Long):String = { requestPage(s"https://www.ebi.ac.uk/europepmc/webservices/rest/MED/$PMID/datalinks?format=json") diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json index 38eb50094..4bee770bd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json @@ -1,6 +1,7 @@ [ - {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, - {"paramName":"i", "paramLongName":"isLookupUrl","paramDescription": "isLookupUrl", "paramRequired": true}, - {"paramName":"w", "paramLongName":"workingPath","paramDescription": "the path of the sequencial file to read", "paramRequired": true}, - {"paramName":"t", "paramLongName":"targetPath","paramDescription": "the oaf path ", "paramRequired": true} + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, + {"paramName":"i", "paramLongName":"isLookupUrl", "paramDescription": "isLookupUrl", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true}, + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the oaf path ", "paramRequired": true}, + {"paramName":"h", "paramLongName":"hdfsServerUri", "paramDescription": "the working path ", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/ebi_download_update.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/ebi_download_update.json index 0ae19234a..0860ed558 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/ebi_download_update.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/ebi_download_update.json @@ -1,5 +1,5 @@ [ - {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, - {"paramName":"s", "paramLongName":"sourcePath","paramDescription": "the source Path", "paramRequired": true}, - {"paramName":"w", "paramLongName":"workingPath","paramDescription": "the working path ", "paramRequired": true} + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, + {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path ", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/workflow.xml index 1fa099ebc..7612321c0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/workflow.xml @@ -25,7 +25,6 @@ Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - yarn-cluster @@ -43,6 +42,7 @@ --workingPath${workingPath} --masteryarn + --hdfsServerUri${nameNode} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/workflow.xml index 1b738caed..cd3bb8c71 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/workflow.xml @@ -1,59 +1,67 @@ - - - - sourcePath - the Working Path - - - workingPath - the Working Path - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - + + + + sourcePath + the Working Path + + + workingPath + the Working Path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + - + - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + - - - yarn-cluster - cluster - Incremental Download EBI Links - eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks - 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}${spark2EventLogDir} - - --sourcePath${sourcePath} - --workingPath${workingPath} - --masteryarn - - - - - - - \ No newline at end of file + + + yarn-cluster + cluster + Incremental Download EBI Links + eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks + dhp-graph-mapper-${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} + + --sourcePath${sourcePath} + --workingPath${workingPath} + --masteryarn + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/BioScholixTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/BioScholixTest.scala index b6058f71b..87279eb21 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/BioScholixTest.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/BioScholixTest.scala @@ -51,12 +51,7 @@ class BioScholixTest extends AbstractVocabularyTest{ } - @Test - def testDownloadEBIUpdate() = { - val data = SparkDownloadEBILinks.requestBaseLineUpdatePage() - println(data) - } - + @Test def testEBIData() = { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/ls_result b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/ls_result new file mode 100644 index 000000000..98a0841c4 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/ls_result @@ -0,0 +1,1433 @@ +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0001.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0002.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0003.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0004.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0005.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0006.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0007.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0008.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0009.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0010.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0011.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0012.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0013.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0014.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0015.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0016.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0017.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0018.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0019.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0020.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0021.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0022.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0023.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0024.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0025.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0026.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0027.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0028.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0029.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0030.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0031.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0032.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0033.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0034.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0035.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0036.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0037.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0038.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0039.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0040.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0041.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0042.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0043.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0044.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0045.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0046.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0047.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0048.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0049.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0050.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0051.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0052.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0053.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0054.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0055.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0056.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0057.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0058.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0059.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0060.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0061.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0062.xml.gz +hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0063.xml.gz 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