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
+hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0064.xml.gz
+hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0065.xml.gz
+hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0066.xml.gz
+hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0067.xml.gz
+hdfs://nameservice1/data/scholix/input/baseline/pubmed21n0068.xml.gz
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+hdfs://nameservice1/data/scholix/input/baseline/pubmed21n1426.xml.gz
+hdfs://nameservice1/data/scholix/input/baseline/pubmed21n1427.xml.gz
+hdfs://nameservice1/data/scholix/input/baseline/pubmed21n1428.xml.gz
+hdfs://nameservice1/data/scholix/input/baseline/pubmed21n1429.xml.gz
+hdfs://nameservice1/data/scholix/input/baseline/pubmed21n1430.xml.gz
+hdfs://nameservice1/data/scholix/input/baseline/pubmed21n1431.xml.gz
+hdfs://nameservice1/data/scholix/input/baseline/pubmed21n1432.xml.gz
+hdfs://nameservice1/data/scholix/input/baseline/pubmed21n1433.xml.gz
\ No newline at end of file