[OC New] last fix

This commit is contained in:
Miriam Baglioni 2024-03-12 23:12:32 +01:00
parent fd34372c40
commit 48c052215c
12 changed files with 316 additions and 26 deletions

View File

@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
return projectScores.map((MapFunction<BipProjectModel, Project>) bipProjectScores -> {
Project project = new Project();
project.setId(bipProjectScores.getProjectId());
// project.setId(bipProjectScores.getProjectId());
project.setMeasures(bipProjectScores.toMeasures());
return project;
}, Encoders.bean(Project.class))

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@ -22,6 +22,7 @@ import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
@ -41,7 +42,9 @@ public class CreateActionSetSparkJob implements Serializable {
private static final String DOI_PREFIX = "50|doi_________::";
private static final String PMID_PREFIX = "50|pmid________::";
private static final String ARXIV_PREFIX = "50|arXiv_______::";
private static final String PMCID_PREFIX = "50|pmcid_______::";
private static final String TRUST = "0.91";
private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
@ -74,25 +77,18 @@ public class CreateActionSetSparkJob implements Serializable {
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final boolean shouldDuplicateRels = Optional
.ofNullable(parser.get("shouldDuplicateRels"))
.map(Boolean::valueOf)
.orElse(Boolean.FALSE);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> extractContent(spark, inputPath, outputPath, shouldDuplicateRels));
spark -> extractContent(spark, inputPath, outputPath));
}
private static void extractContent(SparkSession spark, String inputPath, String outputPath,
boolean shouldDuplicateRels) {
private static void extractContent(SparkSession spark, String inputPath, String outputPath) {
getTextTextJavaPairRDD(spark, inputPath)
// .union(getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, POCI))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);// , GzipCodec.class);
}
private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath) {
@ -115,7 +111,7 @@ public class CreateActionSetSparkJob implements Serializable {
new Text(OBJECT_MAPPER.writeValueAsString(aa))));
}
private static List<Relation> createRelation(COCI value) {
private static List<Relation> createRelation(COCI value) throws JsonProcessingException {
List<Relation> relationList = new ArrayList<>();
@ -131,25 +127,52 @@ public class CreateActionSetSparkJob implements Serializable {
case "pmid":
citing = PMID_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting()));
.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCiting()));
break;
case "arxiv":
citing = ARXIV_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), value.getCiting()));
break;
case "pmcid":
citing = PMCID_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), value.getCiting()));
break;
case "isbn":
case "issn":
return relationList;
default:
throw new IllegalStateException("Invalid prefix: " + value.getCiting_pid());
throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value));
}
switch (value.getCited_pid()) {
case "doi":
cited = DOI_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting()));
.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCited()));
break;
case "pmid":
cited = PMID_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting()));
.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCited()));
break;
case "arxiv":
cited = ARXIV_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), value.getCited()));
break;
case "pmcid":
cited = PMCID_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), value.getCited()));
break;
case "isbn":
case "issn":
return relationList;
default:
throw new IllegalStateException("Invalid prefix: " + value.getCited_pid());
throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value));
}
if (!citing.equals(cited)) {

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@ -9,11 +9,19 @@ import java.util.Arrays;
import java.util.Objects;
import java.util.Optional;
import java.util.stream.Collectors;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
@ -62,6 +70,10 @@ public class MapOCIdsInPids implements Serializable {
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final String nameNode = parser.get("nameNode");
log.info("nameNode {}", nameNode);
unzipCorrespondenceFile(inputPath, nameNode);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
@ -70,6 +82,41 @@ public class MapOCIdsInPids implements Serializable {
}
private static void unzipCorrespondenceFile(String inputPath, String hdfsNameNode) throws IOException {
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
final Path path = new Path(inputPath + "/correspondence/omid.zip");
FileSystem fileSystem = FileSystem.get(conf);
FSDataInputStream project_zip = fileSystem.open(path);
try (ZipInputStream zis = new ZipInputStream(project_zip)) {
ZipEntry entry = null;
while ((entry = zis.getNextEntry()) != null) {
if (!entry.isDirectory()) {
String fileName = entry.getName();
byte buffer[] = new byte[1024];
int count;
try (
FSDataOutputStream out = fileSystem
.create(new Path(inputPath + "/correspondence/omid.csv"))) {
while ((count = zis.read(buffer, 0, buffer.length)) != -1)
out.write(buffer, 0, count);
}
}
}
}
}
private static void mapIdentifiers(SparkSession spark, String inputPath, String outputPath) {
Dataset<COCI> coci = spark
.read()
@ -85,7 +132,7 @@ public class MapOCIdsInPids implements Serializable {
.option("inferSchema", "true")
.option("header", "true")
.option("quotes", "\"")
.load(inputPath + "/correspondence/omid.zip")
.load(inputPath + "/correspondence/omid.csv")
.repartition(5000)
.flatMap((FlatMapFunction<Row, Tuple2<String, String>>) r -> {
String ocIdentifier = r.getAs("omid");
@ -98,7 +145,7 @@ public class MapOCIdsInPids implements Serializable {
}, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
Dataset<COCI> mappedCitingDataset = coci
.joinWith(correspondenceData, coci.col("citing").equalTo(correspondenceData.col("_1")), "left")
.joinWith(correspondenceData, coci.col("citing").equalTo(correspondenceData.col("_1")))
.map((MapFunction<Tuple2<COCI, Tuple2<String, String>>, COCI>) t2 -> {
String correspondent = t2._2()._2();
t2._1().setCiting_pid(correspondent.substring(0, correspondent.indexOf(":")));
@ -118,6 +165,16 @@ public class MapOCIdsInPids implements Serializable {
.mode(SaveMode.Append)
.option("compression", "gzip")
.json(outputPath);
mappedCitingDataset
.joinWith(correspondenceData, mappedCitingDataset.col("cited").equalTo(correspondenceData.col("_1")))
.map((MapFunction<Tuple2<COCI, Tuple2<String, String>>, COCI>) t2 -> {
String correspondent = t2._2()._2();
t2._1().setCited_pid(correspondent.substring(0, correspondent.indexOf(":")));
t2._1().setCited(correspondent.substring(correspondent.indexOf(":") + 1));
return t2._1();
}, Encoders.bean(COCI.class))
.foreach((ForeachFunction<COCI>) c -> System.out.println(OBJECT_MAPPER.writeValueAsString(c)));
}
}

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@ -14,6 +14,7 @@ import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.*;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
@ -79,7 +80,7 @@ public class ReadCOCI implements Serializable {
new Path(workingPath), true);
while (fileStatusListIterator.hasNext()) {
LocatedFileStatus fileStatus = fileStatusListIterator.next();
log.info("extracting file {}", fileStatus.getPath().toString());
Dataset<Row> cociData = spark
.read()
.format("csv")
@ -91,6 +92,7 @@ public class ReadCOCI implements Serializable {
.repartition(100);
cociData.map((MapFunction<Row, COCI>) row -> {
COCI coci = new COCI();
coci.setCiting(row.getString(1));
@ -100,10 +102,12 @@ public class ReadCOCI implements Serializable {
return coci;
}, Encoders.bean(COCI.class))
.filter((FilterFunction<COCI>) c -> c != null)
.write()
.mode(SaveMode.Append)
.option("compression", "gzip")
.json(outputPath);
fileSystem.rename(fileStatus.getPath(), new Path("/tmp/miriam/OC/DONE"));
}
}

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@ -27,6 +27,8 @@ public class COCI implements Serializable {
}
public void setCiting(String citing) {
if (citing != null && citing.startsWith("omid:"))
citing = citing.substring(5);
this.citing = citing;
}
@ -35,6 +37,8 @@ public class COCI implements Serializable {
}
public void setCited(String cited) {
if (cited != null && cited.startsWith("omid:"))
cited = cited.substring(5);
this.cited = cited;
}

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@ -27,6 +27,7 @@
<case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
<case to="extract">${wf:conf('resumeFrom') eq 'ExtractContent'}</case>
<case to="read">${wf:conf('resumeFrom') eq 'ReadContent'}</case>
<case to="remap">${wf:conf('resumeFrom') eq 'MapContent'}</case>
<case to="create_actionset">${wf:conf('resumeFrom') eq 'CreateAS'}</case>
<default to="deleteoutputpath"/> <!-- first action to be done when downloadDump is to be performed -->
</switch>
@ -154,6 +155,7 @@
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}</arg>
<arg>--outputPath</arg><arg>${outputPathExtraction}</arg>
<arg>--nameNode</arg><arg>${nameNode}</arg>
</spark>
<ok to="create_actionset"/>
<error to="Kill"/>

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@ -16,5 +16,10 @@
"paramLongName": "isSparkSessionManged",
"paramDescription": "the hdfs name node",
"paramRequired": false
}
},{
"paramName": "nn",
"paramLongName": "nameNode",
"paramDescription": "the hdfs name node",
"paramRequired": true
}
]

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@ -76,7 +76,7 @@ public class CreateOpenCitationsASTest {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/jsonforas")
.getPath();
CreateActionSetSparkJob
@ -84,8 +84,6 @@ public class CreateOpenCitationsASTest {
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-shouldDuplicateRels",
Boolean.TRUE.toString(),
"-inputPath",
inputPath,
"-outputPath",
@ -99,9 +97,10 @@ public class CreateOpenCitationsASTest {
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
assertEquals(31, tmp.count());
Assertions.assertEquals(27, tmp.count());
tmp.foreach(r -> Assertions.assertEquals(1, r.getCollectedfrom().size()));
// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
}

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@ -0,0 +1,90 @@
package eu.dnetlib.dhp.actionmanager.opencitations;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.LocalFileSystem;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
/**
* @author miriam.baglioni
* @Date 07/03/24
*/
public class RemapTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory
.getLogger(RemapTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(RemapTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(RemapTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(RemapTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void testRemap() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap")
.getPath();
MapOCIdsInPids
.main(
new String[] {
"-isSparkSessionManged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/out/",
"-nameNode", "input1;input2;input3;input4;input5"
});
}
}

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@ -0,0 +1,31 @@
{"cited":"br/061201599020", "citing":"br/06203041400","oci":"oci:06701327944-06504326071"}
{"cited":"br/061201599020","citing":"br/06502272390","oci":"oci:06502272390-061301355525"}
{"cited":"br/061201599020", "citing":"br/06120941789","oci":"oci:0670804699-067055659"}
{"cited":"br/06210273177","citing":"br/06203041400","oci":"oci:061502003994-062201281456"}
{"cited":"br/06210273177", "citing":"br/06502272390","oci":"oci:06502272390-0660806688"}
{"cited":"br/06210273177", "citing":"br/06120941789","oci":"oci:06502307119-0620223645"}
{"cited":"br/0660613430","citing":"br/06203041400","oci":"oci:061502004011-061902692285"}
{"cited":"br/0660613430", "citing":"br/06502272390","oci":"oci:0660549063-0610398792"}
{"cited":"br/0660613430", "citing":"br/06120941789","oci":"oci:06420189324-06301543046"}
{"cited":"br/062602732073","citing":"br/06203041400","oci":"oci:06380130275-061502004367"}
{"cited":"br/062602732073","citing":"br/06502272390","oci":"oci:062403449086-062501448395"}
{"cited":"br/062602732073","citing":"br/06120941789","oci":"oci:06420189328-061202007182"}
{"cited":"br/061103703697","citing":"br/06203041400","oci":"oci:062603906965-061701362658"}
{"cited":"br/061103703697", "citing":"br/06502272390","oci":"oci:0670294309-06104327031"}
{"cited":"br/061103703697","citing":"br/06120941789","oci":"oci:061702060228-061301712529"}
{"cited":"br/06230199640", "citing":"br/0670517081","oci":"oci:06901104174-06503692526"}
{"cited":"br/061703513967","citing":"br/061702310822","oci":"oci:061702310822-061703513967"}
{"cited":"br/062104002953","citing":"br/061702311472","oci":"oci:061702311472-062104002953"}
{"cited":"br/061101204417","citing":"br/062102701590","oci":"oci:062102701590-061101204417"}
{"cited":"br/062403787088","citing":"br/061401499173","oci":"oci:061401499173-062403787088"}
{"cited":"br/061203576338","citing":"br/06110279619","oci":"oci:06110279619-061203576338"}
{"cited":"br/061601962207","citing":"br/061502004018","oci":"oci:061502004018-061601962207"}
{"cited":"br/06101014588", "citing":"br/061502004027","oci":"oci:061502004027-06101014588"}
{"cited":"br/06704040804", "citing":"br/06220799044","oci":"oci:06220799044-06704040804"}
{"cited":"br/061401105151","citing":"br/061502004037","oci":"oci:061502004037-061401105151"}
{"cited":"br/0640821079", "citing":"br/061702311537","oci":"oci:061702311537-0640821079"}
{"cited":"br/06604165310", "citing":"br/062501970289","oci":"oci:062501970289-06604165310"}
{"cited":"br/061501351689","citing":"br/061203895786","oci":"oci:061203895786-061501351689"}
{"cited":"br/06202223692", "citing":"br/06110298832","oci":"oci:06110298832-06202223692"}
{"cited":"br/06104310727", "citing":"br/0660439086","oci":"oci:0660439086-06104310727"}
{"cited":"br/06150216214", "citing":"br/06340150329","oci":"oci:06340150329-06150216214"}

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@ -0,0 +1,48 @@
omid,id
br/061201599020,doi:10.1142/s0219887817501687
br/06203041400,doi:10.1111/j.1523-5378.2005.00327.x pmid:16104945
br/06210273177,doi:10.1090/qam/20394
br/06502272390,pmid:32235596 doi:10.3390/nano10040644
br/0660613430,doi:10.1007/bf00470411
br/06120941789,doi:10.1098/rspa.2006.1747
br/062602732073,doi:10.1007/978-3-642-38844-6_25
br/06230199640,pmid:25088780 doi:10.1016/j.ymeth.2014.07.008
br/061103703697,pmid:2682767
br/0670517081,doi:10.1016/j.foodpol.2021.102189
br/06502310477,doi:10.1142/s0218127416500450
br/06520113284,doi:10.1109/cfasta57821.2023.10243367
br/062303652439,pmid:5962654 doi:10.1016/0020-708x(66)90001-9
br/06250691436,doi:10.1042/bst20150052 pmid:26009172
br/061201665577,doi:10.1097/00115550-200205000-00018
br/06503490336,pmid:34689254 doi:10.1007/s10072-021-05687-0
br/06220615942,pmid:25626134 doi:10.1016/j.jcis.2015.01.008
br/061103389243,doi:10.4324/9780203702819-10
br/062303011271,doi:10.1109/icassp.2011.5946250
br/061302926083,doi:10.4018/978-1-6684-3937-1.ch002
br/061402485360,doi:10.1109/iciict.2015.7396079
br/06410101083,doi:10.1016/j.autcon.2023.104828
br/062202243386,doi:10.1016/0001-8791(81)90022-1
br/06170421486,doi:10.1130/0016-7606(2003)115<0166:dsagmf>2.0.co;2
br/061201983865,doi:10.4324/9781315109008 isbn:9781315109008
br/061701697230,doi:10.1016/j.trd.2012.07.006
br/061201137111,doi:10.1109/access.2020.2971656
br/06120436283,pmid:2254430 doi:10.1128/jcm.28.11.2551-2554.1990
br/061903968916,doi:10.1111/j.1742-1241.1988.tb08627.x
br/06201583482,doi:10.1016/0016-5085(78)93139-6
br/06130338317,doi:10.2134/agronj1952.00021962004400080013x
br/062601538320,doi:10.1371/journal.pone.0270593 pmid:35789338
br/062401098626,pmid:22385804 doi:10.1016/j.talanta.2011.12.034
br/06190436492,doi:10.1039/c7dt01499f pmid:28644489
br/06202819247,doi:10.1007/978-3-319-45823-6_57
br/0648013560,doi:10.1080/14772000.2012.705356
br/0690214059,doi:10.2752/175630608x329217
br/06601640415,doi:10.1080/18128600508685647
br/061503394761,doi:10.1002/0471443395.img018
br/061702861849,pmid:31203682 doi:10.1080/10428194.2019.1627538
br/06450133713,doi:10.1093/acprof:oso/9780199670888.003.0008
br/0628074892,doi:10.1097/hnp.0000000000000597
br/061601032219,doi:10.1002/bdm.2102
br/06602079930,doi:10.1101/2020.08.25.267500
br/0604192147,doi:10.11501/3307395
br/061101933800,doi:10.1142/s0217732398002242
br/06504184118,pmid:10091417
1 omid id
2 br/061201599020 doi:10.1142/s0219887817501687
3 br/06203041400 doi:10.1111/j.1523-5378.2005.00327.x pmid:16104945
4 br/06210273177 doi:10.1090/qam/20394
5 br/06502272390 pmid:32235596 doi:10.3390/nano10040644
6 br/0660613430 doi:10.1007/bf00470411
7 br/06120941789 doi:10.1098/rspa.2006.1747
8 br/062602732073 doi:10.1007/978-3-642-38844-6_25
9 br/06230199640 pmid:25088780 doi:10.1016/j.ymeth.2014.07.008
10 br/061103703697 pmid:2682767
11 br/0670517081 doi:10.1016/j.foodpol.2021.102189
12 br/06502310477 doi:10.1142/s0218127416500450
13 br/06520113284 doi:10.1109/cfasta57821.2023.10243367
14 br/062303652439 pmid:5962654 doi:10.1016/0020-708x(66)90001-9
15 br/06250691436 doi:10.1042/bst20150052 pmid:26009172
16 br/061201665577 doi:10.1097/00115550-200205000-00018
17 br/06503490336 pmid:34689254 doi:10.1007/s10072-021-05687-0
18 br/06220615942 pmid:25626134 doi:10.1016/j.jcis.2015.01.008
19 br/061103389243 doi:10.4324/9780203702819-10
20 br/062303011271 doi:10.1109/icassp.2011.5946250
21 br/061302926083 doi:10.4018/978-1-6684-3937-1.ch002
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