[OpenCitation] change to extract in json format each folder just onece
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fbc28ee8c3
commit
b071f8e415
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@ -41,18 +41,14 @@ public class ReadCOCI implements Serializable {
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final String hdfsNameNode = parser.get("nameNode");
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log.info("nameNode: {}", hdfsNameNode);
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final String inputPath = parser.get("sourcePath");
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log.info("input path : {}", inputPath);
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final String[] inputFile = parser.get("inputFile").split(";");
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log.info("inputFile {}", inputFile.toString());
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Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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final String workingPath = parser.get("workingPath");
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log.info("workingPath {}", workingPath);
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FileSystem fileSystem = FileSystem.get(conf);
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SparkConf sconf = new SparkConf();
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final String delimiter = Optional
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@ -65,25 +61,20 @@ public class ReadCOCI implements Serializable {
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spark -> {
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doRead(
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spark,
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fileSystem,
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inputPath,
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workingPath,
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inputFile,
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outputPath,
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delimiter);
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});
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}
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public static void doRead(SparkSession spark, FileSystem fileSystem, String inputPath, String outputPath,
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private static void doRead(SparkSession spark, String workingPath, String[] inputFiles,
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String outputPath,
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String delimiter) throws IOException {
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RemoteIterator<LocatedFileStatus> iterator = fileSystem
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.listFiles(
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new Path(inputPath), true);
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for(String inputFile : inputFiles){
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String p_string = workingPath + "/" + inputFile ;
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while (iterator.hasNext()) {
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LocatedFileStatus fileStatus = iterator.next();
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Path p = fileStatus.getPath();
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String p_string = p.toString();
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Dataset<Row> cociData = spark
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.read()
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.format("csv")
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@ -91,7 +82,8 @@ public class ReadCOCI implements Serializable {
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.option("inferSchema", "true")
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.option("header", "true")
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.option("quotes", "\"")
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.load(p_string);
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.load(p_string)
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.repartition(100);
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cociData.map((MapFunction<Row, COCI>) row -> {
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COCI coci = new COCI();
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@ -103,7 +95,7 @@ public class ReadCOCI implements Serializable {
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath + "/" + p_string.substring(p_string.lastIndexOf("/") + 1));
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.json(outputPath + inputFile);
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}
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}
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@ -1,17 +1,12 @@
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[
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{
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"paramName": "sp",
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"paramLongName": "sourcePath",
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"paramName": "wp",
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"paramLongName": "workingPath",
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"paramDescription": "the zipped opencitations file",
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"paramRequired": true
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},
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{
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"paramName": "nn",
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"paramLongName": "nameNode",
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"paramDescription": "the hdfs name node",
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"paramRequired": true
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},
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{
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"paramName": "issm",
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"paramLongName": "isSparkSessionManaged",
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@ -28,7 +23,13 @@
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"paramName": "op",
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"paramLongName": "outputPath",
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"paramDescription": "the hdfs name node",
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"paramRequired": false
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"paramRequired": true
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},
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{
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"paramName": "if",
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"paramLongName": "inputFile",
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"paramDescription": "the hdfs name node",
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"paramRequired": true
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}
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]
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@ -82,10 +82,10 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${workingPath}/COCI</arg>
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<arg>--outputPath</arg><arg>${workingDir}/COCI</arg>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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<arg>--workingPath</arg><arg>${workingPath}/COCI</arg>
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<arg>--outputPath</arg><arg>${workingPath}/COCI_JSON</arg>
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<arg>--delimiter</arg><arg>${delimiter}</arg>
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<arg>--inputFile</arg><arg>${inputFileCoci}</arg>
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</spark>
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<ok to="create_actionset"/>
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<error to="Kill"/>
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@ -108,7 +108,7 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--inputPath</arg><arg>${workingPath}/COCI</arg>
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<arg>--inputPath</arg><arg>${workingPath}/COCI_JSON</arg>
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<arg>--outputPath</arg><arg>${outputPath}</arg>
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</spark>
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<ok to="End"/>
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@ -10,6 +10,7 @@ import java.nio.file.Path;
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import org.apache.commons.io.FileUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.LocalFileSystem;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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@ -73,15 +74,53 @@ public class ReadCOCITest {
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"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
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.getPath();
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LocalFileSystem fs = FileSystem.getLocal(new Configuration());
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fs
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.copyFromLocalFile(
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false, new org.apache.hadoop.fs.Path(getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input1")
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.getPath()),
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new org.apache.hadoop.fs.Path(workingDir + "/COCI/input1"));
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fs
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.copyFromLocalFile(
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false, new org.apache.hadoop.fs.Path(getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input2")
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.getPath()),
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new org.apache.hadoop.fs.Path(workingDir + "/COCI/input2"));
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fs
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.copyFromLocalFile(
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false, new org.apache.hadoop.fs.Path(getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input3")
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.getPath()),
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new org.apache.hadoop.fs.Path(workingDir + "/COCI/input3"));
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fs
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.copyFromLocalFile(
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false, new org.apache.hadoop.fs.Path(getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input4")
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.getPath()),
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new org.apache.hadoop.fs.Path(workingDir + "/COCI/input4"));
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ReadCOCI
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.doRead(
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spark, FileSystem.getLocal(new Configuration()), inputPath,
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workingDir.toString() + "/COCI", DEFAULT_DELIMITER);
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.main(
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new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-workingPath",
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workingDir.toString() + "/COCI",
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"-outputPath",
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workingDir.toString() + "/COCI_json/",
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"-inputFile", "input1;input2;input3;input4"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<COCI> tmp = sc
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.textFile(workingDir.toString() + "/COCI/*/")
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.textFile(workingDir.toString() + "/COCI_json/*/")
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.map(item -> OBJECT_MAPPER.readValue(item, COCI.class));
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Assertions.assertEquals(23, tmp.count());
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