merged from master

This commit is contained in:
Claudio Atzori 2021-03-08 15:44:34 +01:00
commit 8d2bb24512
161 changed files with 9642 additions and 979 deletions

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@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.merge;
import java.text.Normalizer;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
@ -32,27 +33,33 @@ public class AuthorMerger {
}
public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b) {
public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b, Double threshold) {
int pa = countAuthorsPids(a);
int pb = countAuthorsPids(b);
List<Author> base, enrich;
int sa = authorsSize(a);
int sb = authorsSize(b);
if (pa == pb) {
base = sa > sb ? a : b;
enrich = sa > sb ? b : a;
} else {
if (sa == sb) {
base = pa > pb ? a : b;
enrich = pa > pb ? b : a;
} else {
base = sa > sb ? a : b;
enrich = sa > sb ? b : a;
}
enrichPidFromList(base, enrich);
enrichPidFromList(base, enrich, threshold);
return base;
}
private static void enrichPidFromList(List<Author> base, List<Author> enrich) {
public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b) {
return mergeAuthor(a, b, THRESHOLD);
}
private static void enrichPidFromList(List<Author> base, List<Author> enrich, Double threshold) {
if (base == null || enrich == null)
return;
// <pidComparableString, Author> (if an Author has more than 1 pid, it appears 2 times in the list)
final Map<String, Author> basePidAuthorMap = base
.stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0)
@ -63,6 +70,7 @@ public class AuthorMerger {
.map(p -> new Tuple2<>(pidToComparableString(p), a)))
.collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1));
// <pid, Author> (list of pid that are missing in the other list)
final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich
.stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0)
@ -83,10 +91,10 @@ public class AuthorMerger {
.max(Comparator.comparing(Tuple2::_1));
if (simAuthor.isPresent()) {
double th = THRESHOLD;
double th = threshold;
// increase the threshold if the surname is too short
if (simAuthor.get()._2().getSurname() != null
&& simAuthor.get()._2().getSurname().length() <= 3)
&& simAuthor.get()._2().getSurname().length() <= 3 && threshold > 0.0)
th = 0.99;
if (simAuthor.get()._1() > th) {
@ -156,7 +164,7 @@ public class AuthorMerger {
}
private static String normalize(final String s) {
return nfd(s)
String[] normalized = nfd(s)
.toLowerCase()
// do not compact the regexes in a single expression, would cause StackOverflowError
// in case
@ -166,7 +174,12 @@ public class AuthorMerger {
.replaceAll("(\\p{Punct})+", " ")
.replaceAll("(\\d)+", " ")
.replaceAll("(\\n)+", " ")
.trim();
.trim()
.split(" ");
Arrays.sort(normalized);
return String.join(" ", normalized);
}
private static String nfd(final String s) {

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@ -0,0 +1,100 @@
package eu.dnetlib.dhp.oa.merge;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
public class AuthorMergerTest {
private String publicationsBasePath;
private List<List<Author>> authors;
@BeforeEach
public void setUp() throws Exception {
publicationsBasePath = Paths
.get(AuthorMergerTest.class.getResource("/eu/dnetlib/dhp/oa/merge").toURI())
.toFile()
.getAbsolutePath();
authors = readSample(publicationsBasePath + "/publications_with_authors.json", Publication.class)
.stream()
.map(p -> p._2().getAuthor())
.collect(Collectors.toList());
}
@Test
public void mergeTest() { // used in the dedup: threshold set to 0.95
for (List<Author> authors1 : authors) {
System.out.println("List " + (authors.indexOf(authors1) + 1));
for (Author author : authors1) {
System.out.println(authorToString(author));
}
}
List<Author> merge = AuthorMerger.merge(authors);
System.out.println("Merge ");
for (Author author : merge) {
System.out.println(authorToString(author));
}
Assertions.assertEquals(7, merge.size());
}
public <T> List<Tuple2<String, T>> readSample(String path, Class<T> clazz) {
List<Tuple2<String, T>> res = new ArrayList<>();
BufferedReader reader;
try {
reader = new BufferedReader(new FileReader(path));
String line = reader.readLine();
while (line != null) {
res
.add(
new Tuple2<>(
MapDocumentUtil.getJPathString("$.id", line),
new ObjectMapper().readValue(line, clazz)));
// read next line
line = reader.readLine();
}
reader.close();
} catch (IOException e) {
e.printStackTrace();
}
return res;
}
public String authorToString(Author a) {
String print = "Fullname = ";
print += a.getFullname() + " pid = [";
if (a.getPid() != null)
for (StructuredProperty sp : a.getPid()) {
print += sp.toComparableString() + " ";
}
print += "]";
return print;
}
}

File diff suppressed because one or more lines are too long

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@ -108,6 +108,8 @@ public class ModelConstants {
public static final KeyValue UNKNOWN_REPOSITORY = keyValue(
"10|openaire____::55045bd2a65019fd8e6741a755395c8c", "Unknown Repository");
public static final Qualifier UNKNOWN_COUNTRY = qualifier(UNKNOWN, "Unknown", DNET_COUNTRY_TYPE, DNET_COUNTRY_TYPE);
private static Qualifier qualifier(
final String classid,
final String classname,

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@ -3,6 +3,9 @@ package eu.dnetlib.dhp.schema.common;
import static com.google.common.base.Preconditions.checkArgument;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
@ -473,4 +476,25 @@ public class ModelSupport {
private static <T extends Oaf> String idFnForOafEntity(T t) {
return ((OafEntity) t).getId();
}
public static final String ISO8601FORMAT = "yyyy-MM-dd'T'HH:mm:ssZ";
public static String oldest(String dateA, String dateB) throws ParseException {
if (StringUtils.isBlank(dateA)) {
return dateB;
}
if (StringUtils.isBlank(dateB)) {
return dateA;
}
if (StringUtils.isNotBlank(dateA) && StringUtils.isNotBlank(dateB)) {
final Date a = new SimpleDateFormat(ISO8601FORMAT).parse(dateA);
final Date b = new SimpleDateFormat(ISO8601FORMAT).parse(dateB);
return a.before(b) ? dateA : dateB;
} else {
return null;
}
}
}

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@ -1,7 +1,6 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
import java.util.List;
import com.google.common.base.Objects;
@ -9,7 +8,7 @@ import com.google.common.base.Objects;
/**
* Represent a measure, must be further described by a system available resource providing name and descriptions.
*/
public class Measure implements Serializable {
public class Measure {
/**
* Unique measure identifier.
@ -17,7 +16,7 @@ public class Measure implements Serializable {
private String id;
/**
* List of units associated with this measure. KeyValue provides a pair to store the label (key) and the value, plus
* List of units associated with this measure. KeyValue provides a pair to store the laber (key) and the value, plus
* common provenance information.
*/
private List<KeyValue> unit;

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@ -62,8 +62,6 @@ public abstract class Oaf implements Serializable {
.distinct() // relies on KeyValue.equals
.collect(Collectors.toList()));
mergeOAFDataInfo(o);
setLastupdatetimestamp(
Math
.max(

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@ -351,8 +351,6 @@ public class Project extends OafEntity implements Serializable {
? p.getFundedamount()
: fundedamount;
// programme = mergeLists(programme, p.getProgramme());
h2020classification = mergeLists(h2020classification, p.getH2020classification());
mergeOAFDataInfo(e);

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@ -1,8 +1,11 @@
package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import static com.google.common.base.Preconditions.checkArgument;
import java.text.ParseException;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
@ -106,7 +109,7 @@ public class Relation extends Oaf {
}
public Boolean getValidated() {
return validated;
return Objects.nonNull(validated) && validated;
}
public void setValidated(Boolean validated) {
@ -130,6 +133,13 @@ public class Relation extends Oaf {
Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal");
checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal");
setValidated(getValidated() || r.getValidated());
try {
setValidationDate(ModelSupport.oldest(getValidationDate(), r.getValidationDate()));
} catch (ParseException e) {
throw new IllegalArgumentException(String.format("invalid validation date format in relation [s:%s, t:%s]: %s", getSource(), getTarget(), getValidationDate()));
}
super.mergeFrom(r);
}

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@ -243,7 +243,7 @@ public class Result extends OafEntity implements Serializable {
Result r = (Result) e;
// TODO consider merging also Measures
measures = mergeLists(measures, r.getMeasures());
instance = mergeLists(instance, r.getInstance());
@ -323,13 +323,13 @@ public class Result extends OafEntity implements Serializable {
if (a.size() == b.size()) {
int msa = a
.stream()
.filter(i -> i.getValue() != null)
.filter(i -> i != null && i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);
int msb = b
.stream()
.filter(i -> i.getValue() != null)
.filter(i -> i != null && i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);

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@ -63,6 +63,51 @@ public class MergeTest {
assertEquals(3, a.getSubject().size());
}
@Test
public void mergeRelationTest() {
Relation a = createRel(null, null);
Relation b = createRel(null, null);
a.mergeFrom(b);
assertEquals(a, b);
a = createRel(true, null);
b = createRel(null, null);
a.mergeFrom(b);
assertEquals(true, a.getValidated());
a = createRel(true, null);
b = createRel(false, null);
a.mergeFrom(b);
assertEquals(true, a.getValidated());
a = createRel(true, null);
b = createRel(true, "2016-04-05T12:41:19.202Z");
a.mergeFrom(b);
assertEquals("2016-04-05T12:41:19.202Z", a.getValidationDate());
}
@Test
public void mergeRelationTestParseException() {
assertThrows(IllegalArgumentException.class, () -> {
Relation a = createRel(true, "2016-04-05");
Relation b = createRel(true, "2016-04-05");
a.mergeFrom(b);
});
}
private Relation createRel(Boolean validated, String validationDate) {
Relation rel = new Relation();
rel.setSource("1");
rel.setTarget("2");
rel.setRelType("reltype");
rel.setSubRelType("subreltype");
rel.setRelClass("relclass");
rel.setValidated(validated);
rel.setValidationDate(validationDate);
return rel;
}
private KeyValue setKV(final String key, final String value) {
KeyValue k = new KeyValue();

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@ -125,16 +125,17 @@ public class SparkAtomicActionScoreJob implements Serializable {
return ret;
}, Encoders.bean(BipScore.class))
.groupByKey((MapFunction<BipScore, String>) value -> value.getId(), Encoders.STRING())
.mapGroups((MapGroupsFunction<String, BipScore, I>) (k, it) -> {
Result ret = inputClazz.newInstance();
.mapGroups((MapGroupsFunction<String, BipScore, Result>) (k, it) -> {
Result ret = new Result();
ret.setDataInfo(getDataInfo());
BipScore first = it.next();
ret.setId(first.getId());
ret.setMeasures(getMeasure(first));
it.forEachRemaining(value -> ret.getMeasures().addAll(getMeasure(value)));
return (I) ret;
}, Encoders.bean(inputClazz))
return ret;
}, Encoders.bean(Result.class))
.toJavaRDD()
.map(p -> new AtomicAction(inputClazz, p))
.mapToPair(

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@ -1,20 +1,20 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
}
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
}
]

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@ -1,22 +1,22 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
},
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
},
{
"paramName": "rtn",
"paramLongName": "resultTableName",

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@ -21,10 +21,10 @@
</kill>
<action name="deleteoutputpath">
<fs>
<delete path='${outputPath}'/>
<mkdir path='${outputPath}'/>
<delete path='${workingDir}'/>
<mkdir path='${workingDir}'/>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
<delete path="${workingDir}"/>
<mkdir path="${workingDir}"/>
</fs>
<ok to="atomicactions"/>
<error to="Kill"/>

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@ -5,18 +5,12 @@ import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
@ -31,9 +25,7 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import scala.Tuple2;
import eu.dnetlib.dhp.schema.oaf.Publication;
public class SparkAtomicActionScoreJobTest {

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@ -32,15 +32,15 @@ public class CheckDuplictedIdsJob {
IOUtils
.toString(
CheckDuplictedIdsJob.class
.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json")));
.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/check_duplicates.json")));
parser.parseArgument(args);
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String countPath = parser.get("workingPath") + "/counts";
final String countPath = parser.get("outputDir") + "/counts";
log.info("countPath: {}", countPath);
final SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
@ -59,6 +59,7 @@ public class CheckDuplictedIdsJob {
.map(o -> ClusterUtils.incrementAccumulator(o, total), Encoders.tuple(Encoders.STRING(), Encoders.LONG()))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(countPath);
;

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@ -44,10 +44,10 @@ public class GenerateEventsJob {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String eventsPath = workingPath + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final Set<String> dsIdWhitelist = ClusterUtils.parseParamAsList(parser, "datasourceIdWhitelist");
@ -59,6 +59,9 @@ public class GenerateEventsJob {
final Set<String> dsIdBlacklist = ClusterUtils.parseParamAsList(parser, "datasourceIdBlacklist");
log.info("datasourceIdBlacklist: {}", StringUtils.join(dsIdBlacklist, ","));
final Set<String> topicWhitelist = ClusterUtils.parseParamAsList(parser, "topicWhitelist");
log.info("topicWhitelist: {}", StringUtils.join(topicWhitelist, ","));
final SparkConf conf = new SparkConf();
runWithSparkSession(conf, isSparkSessionManaged, spark -> {
@ -70,12 +73,12 @@ public class GenerateEventsJob {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_events");
final Dataset<ResultGroup> groups = ClusterUtils
.readPath(spark, workingPath + "/duplicates", ResultGroup.class);
.readPath(spark, workingDir + "/duplicates", ResultGroup.class);
final Dataset<Event> dataset = groups
.map(
g -> EventFinder
.generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators),
.generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, topicWhitelist, accumulators),
Encoders
.bean(EventGroup.class))
.flatMap(g -> g.getData().iterator(), Encoders.bean(Event.class));

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@ -46,7 +46,7 @@ public class GenerateStatsJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String dbUrl = parser.get("dbUrl");

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@ -46,7 +46,7 @@ public class IndexEventSubsetJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String index = parser.get("index");
@ -55,6 +55,18 @@ public class IndexEventSubsetJob {
final String indexHost = parser.get("esHost");
log.info("indexHost: {}", indexHost);
final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount");
log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount);
final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait");
log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait);
final String esBatchSizeEntries = parser.get("esBatchSizeEntries");
log.info("esBatchSizeEntries: {}", esBatchSizeEntries);
final String esNodesWanOnly = parser.get("esNodesWanOnly");
log.info("esNodesWanOnly: {}", esNodesWanOnly);
final int maxEventsForTopic = NumberUtils.toInt(parser.get("maxEventsForTopic"));
log.info("maxEventsForTopic: {}", maxEventsForTopic);
@ -86,10 +98,10 @@ public class IndexEventSubsetJob {
esCfg.put("es.index.auto.create", "false");
esCfg.put("es.nodes", indexHost);
esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY
esCfg.put("es.batch.write.retry.count", "8");
esCfg.put("es.batch.write.retry.wait", "60s");
esCfg.put("es.batch.size.entries", "200");
esCfg.put("es.nodes.wan.only", "true");
esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
esCfg.put("es.batch.size.entries", esBatchSizeEntries);
esCfg.put("es.nodes.wan.only", esNodesWanOnly);
log.info("*** Start indexing");
JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);

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@ -54,7 +54,7 @@ public class IndexNotificationsJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String index = parser.get("index");
@ -63,6 +63,18 @@ public class IndexNotificationsJob {
final String indexHost = parser.get("esHost");
log.info("indexHost: {}", indexHost);
final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount");
log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount);
final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait");
log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait);
final String esBatchSizeEntries = parser.get("esBatchSizeEntries");
log.info("esBatchSizeEntries: {}", esBatchSizeEntries);
final String esNodesWanOnly = parser.get("esNodesWanOnly");
log.info("esNodesWanOnly: {}", esNodesWanOnly);
final String brokerApiBaseUrl = parser.get("brokerApiBaseUrl");
log.info("brokerApiBaseUrl: {}", brokerApiBaseUrl);
@ -92,10 +104,10 @@ public class IndexNotificationsJob {
esCfg.put("es.index.auto.create", "false");
esCfg.put("es.nodes", indexHost);
esCfg.put("es.mapping.id", "notificationId"); // THE PRIMARY KEY
esCfg.put("es.batch.write.retry.count", "8");
esCfg.put("es.batch.write.retry.wait", "60s");
esCfg.put("es.batch.size.entries", "200");
esCfg.put("es.nodes.wan.only", "true");
esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
esCfg.put("es.batch.size.entries", esBatchSizeEntries);
esCfg.put("es.nodes.wan.only", esNodesWanOnly);
log.info("*** Start indexing");
JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);

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@ -36,7 +36,7 @@ public class IndexOnESJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String index = parser.get("index");
@ -45,6 +45,18 @@ public class IndexOnESJob {
final String indexHost = parser.get("esHost");
log.info("indexHost: {}", indexHost);
final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount");
log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount);
final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait");
log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait);
final String esBatchSizeEntries = parser.get("esBatchSizeEntries");
log.info("esBatchSizeEntries: {}", esBatchSizeEntries);
final String esNodesWanOnly = parser.get("esNodesWanOnly");
log.info("esNodesWanOnly: {}", esNodesWanOnly);
final SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
final JavaRDD<String> inputRdd = ClusterUtils
@ -53,15 +65,13 @@ public class IndexOnESJob {
.javaRDD();
final Map<String, String> esCfg = new HashMap<>();
// esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54");
esCfg.put("es.index.auto.create", "false");
esCfg.put("es.nodes", indexHost);
esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY
esCfg.put("es.batch.write.retry.count", "8");
esCfg.put("es.batch.write.retry.wait", "60s");
esCfg.put("es.batch.size.entries", "200");
esCfg.put("es.nodes.wan.only", "true");
esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
esCfg.put("es.batch.size.entries", esBatchSizeEntries);
esCfg.put("es.nodes.wan.only", esNodesWanOnly);
JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);
}

View File

@ -42,10 +42,10 @@ public class JoinStep0Job {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step0";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step0";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -57,10 +57,10 @@ public class JoinStep0Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/simpleEntities", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/simpleEntities", OaBrokerMainEntity.class);
final Dataset<RelatedDatasource> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedDatasources", RelatedDatasource.class);
.readPath(spark, workingDir + "/relatedDatasources", RelatedDatasource.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedDatasource>, OaBrokerMainEntity> aggr = new RelatedDatasourceAggregator()
.toColumn();

View File

@ -40,10 +40,10 @@ public class JoinStep1Job {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step1";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step1";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -55,10 +55,10 @@ public class JoinStep1Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step0", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step0", OaBrokerMainEntity.class);
final Dataset<RelatedProject> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedProjects", RelatedProject.class);
.readPath(spark, workingDir + "/relatedProjects", RelatedProject.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedProject>, OaBrokerMainEntity> aggr = new RelatedProjectAggregator()
.toColumn();

View File

@ -39,10 +39,10 @@ public class JoinStep2Job {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step2";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step2";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -54,10 +54,10 @@ public class JoinStep2Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step1", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step1", OaBrokerMainEntity.class);
final Dataset<RelatedSoftware> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedSoftwares", RelatedSoftware.class);
.readPath(spark, workingDir + "/relatedSoftwares", RelatedSoftware.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedSoftware>, OaBrokerMainEntity> aggr = new RelatedSoftwareAggregator()
.toColumn();

View File

@ -40,10 +40,10 @@ public class JoinStep3Job {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step3";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step3";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -55,10 +55,10 @@ public class JoinStep3Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step2", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step2", OaBrokerMainEntity.class);
final Dataset<RelatedDataset> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedDatasets", RelatedDataset.class);
.readPath(spark, workingDir + "/relatedDatasets", RelatedDataset.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedDataset>, OaBrokerMainEntity> aggr = new RelatedDatasetAggregator()
.toColumn();

View File

@ -40,10 +40,10 @@ public class JoinStep4Job {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step4";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step4";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -55,10 +55,10 @@ public class JoinStep4Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step3", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step3", OaBrokerMainEntity.class);
final Dataset<RelatedPublication> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedPublications", RelatedPublication.class);
.readPath(spark, workingDir + "/relatedPublications", RelatedPublication.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedPublication>, OaBrokerMainEntity> aggr = new RelatedPublicationAggregator()
.toColumn();

View File

@ -36,7 +36,7 @@ import eu.dnetlib.dhp.broker.oa.util.ClusterUtils;
public class PartitionEventsByDsIdJob {
private static final Logger log = LoggerFactory.getLogger(PartitionEventsByDsIdJob.class);
private static final String OPENDOAR_NSPREFIX = "10|opendoar____::";
private static final String OPENDOAR_NSPREFIX = "opendoar____::";
public static void main(final String[] args) throws Exception {
@ -55,10 +55,10 @@ public class PartitionEventsByDsIdJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String partitionPath = parser.get("workingPath") + "/eventsByOpendoarId";
final String partitionPath = parser.get("outputDir") + "/eventsByOpendoarId";
log.info("partitionPath: {}", partitionPath);
final String opendoarIds = parser.get("opendoarIds");
@ -91,6 +91,7 @@ public class PartitionEventsByDsIdJob {
.write()
.partitionBy("group")
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(partitionPath);
});
@ -122,6 +123,7 @@ public class PartitionEventsByDsIdJob {
final ShortEventMessageWithGroupId res = new ShortEventMessageWithGroupId();
res.setEventId(e.getEventId());
res.setOriginalId(payload.getResult().getOriginalId());
res.setTitle(payload.getResult().getTitles().stream().filter(StringUtils::isNotBlank).findFirst().orElse(null));
res.setTopic(e.getTopic());

View File

@ -45,10 +45,10 @@ public class PrepareGroupsJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String groupsPath = workingPath + "/duplicates";
final String groupsPath = workingDir + "/duplicates";
log.info("groupsPath: {}", groupsPath);
final SparkConf conf = new SparkConf();
@ -60,10 +60,10 @@ public class PrepareGroupsJob {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_groups");
final Dataset<OaBrokerMainEntity> results = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step4", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step4", OaBrokerMainEntity.class);
final Dataset<Relation> mergedRels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS));
final TypedColumn<Tuple2<OaBrokerMainEntity, Relation>, ResultGroup> aggr = new ResultAggregator()

View File

@ -42,10 +42,10 @@ public class PrepareRelatedDatasetsJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedDatasets";
final String relsPath = workingDir + "/relatedDatasets";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();
@ -62,7 +62,7 @@ public class PrepareRelatedDatasetsJob {
.map(ConversionUtils::oafDatasetToBrokerDataset, Encoders.bean(OaBrokerRelatedDataset.class));
final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
.filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass()))
@ -72,7 +72,8 @@ public class PrepareRelatedDatasetsJob {
final Dataset<RelatedDataset> dataset = rels
.joinWith(datasets, datasets.col("openaireId").equalTo(rels.col("target")), "inner")
.map(t -> {
final RelatedDataset rel = new RelatedDataset(t._1.getSource(), t._2);
final RelatedDataset rel = new RelatedDataset(t._1.getSource(),
t._2);
rel.getRelDataset().setRelType(t._1.getRelClass());
return rel;
}, Encoders.bean(RelatedDataset.class));

View File

@ -48,10 +48,10 @@ public class PrepareRelatedDatasourcesJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedDatasources";
final String relsPath = workingDir + "/relatedDatasources";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();

View File

@ -44,10 +44,10 @@ public class PrepareRelatedProjectsJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedProjects";
final String relsPath = workingDir + "/relatedProjects";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();
@ -64,7 +64,7 @@ public class PrepareRelatedProjectsJob {
.map(ConversionUtils::oafProjectToBrokerProject, Encoders.bean(OaBrokerProject.class));
final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT))
.filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS))

View File

@ -43,10 +43,10 @@ public class PrepareRelatedPublicationsJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedPublications";
final String relsPath = workingDir + "/relatedPublications";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();
@ -65,7 +65,7 @@ public class PrepareRelatedPublicationsJob {
Encoders.bean(OaBrokerRelatedPublication.class));
final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
.filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass()))
@ -75,7 +75,8 @@ public class PrepareRelatedPublicationsJob {
final Dataset<RelatedPublication> dataset = rels
.joinWith(pubs, pubs.col("openaireId").equalTo(rels.col("target")), "inner")
.map(t -> {
final RelatedPublication rel = new RelatedPublication(t._1.getSource(), t._2);
final RelatedPublication rel = new RelatedPublication(
t._1.getSource(), t._2);
rel.getRelPublication().setRelType(t._1.getRelClass());
return rel;
}, Encoders.bean(RelatedPublication.class));

View File

@ -44,10 +44,10 @@ public class PrepareRelatedSoftwaresJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedSoftwares";
final String relsPath = workingDir + "/relatedSoftwares";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();
@ -64,7 +64,7 @@ public class PrepareRelatedSoftwaresJob {
.map(ConversionUtils::oafSoftwareToBrokerSoftware, Encoders.bean(OaBrokerRelatedSoftware.class));
final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
.filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS))

View File

@ -44,10 +44,10 @@ public class PrepareSimpleEntititiesJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String simpleEntitiesPath = workingPath + "/simpleEntities";
final String simpleEntitiesPath = workingDir + "/simpleEntities";
log.info("simpleEntitiesPath: {}", simpleEntitiesPath);
final SparkConf conf = new SparkConf();

View File

@ -16,7 +16,24 @@ public class EnrichMissingSubject extends UpdateMatcher<OaBrokerTypedValue> {
public EnrichMissingSubject() {
super(20,
s -> Topic.fromPath("ENRICH/MISSING/SUBJECT/" + s.getType()),
s -> {
switch (s.getType().toLowerCase()) {
case "acm":
return Topic.ENRICH_MISSING_SUBJECT_ACM;
case "arxiv":
return Topic.ENRICH_MISSING_SUBJECT_ARXIV;
case "ddc":
return Topic.ENRICH_MISSING_SUBJECT_DDC;
case "jel":
return Topic.ENRICH_MISSING_SUBJECT_JEL;
case "mesh":
return Topic.ENRICH_MISSING_SUBJECT_MESHEUROPMC;
case "rvk":
return Topic.ENRICH_MISSING_SUBJECT_RVK;
default:
return null;
}
},
(p, s) -> p.getSubjects().add(s),
s -> subjectAsString(s));
}

View File

@ -16,7 +16,24 @@ public class EnrichMoreSubject extends UpdateMatcher<OaBrokerTypedValue> {
public EnrichMoreSubject() {
super(20,
s -> Topic.fromPath("ENRICH/MORE/SUBJECT/" + s.getType()),
s -> {
switch (s.getType().toLowerCase()) {
case "acm":
return Topic.ENRICH_MORE_SUBJECT_ACM;
case "arxiv":
return Topic.ENRICH_MORE_SUBJECT_ARXIV;
case "ddc":
return Topic.ENRICH_MORE_SUBJECT_DDC;
case "jel":
return Topic.ENRICH_MORE_SUBJECT_JEL;
case "mesh":
return Topic.ENRICH_MORE_SUBJECT_MESHEUROPMC;
case "rvk":
return Topic.ENRICH_MORE_SUBJECT_RVK;
default:
return null;
}
},
(p, s) -> p.getSubjects().add(s),
s -> subjectAsString(s));
}

View File

@ -17,6 +17,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class ClusterUtils {
@ -30,6 +31,16 @@ public class ClusterUtils {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
public static Dataset<Relation> loadRelations(final String graphPath, final SparkSession spark) {
return ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.map(r -> {
r.setSource(ConversionUtils.cleanOpenaireId(r.getSource()));
r.setTarget(ConversionUtils.cleanOpenaireId(r.getTarget()));
return r;
}, Encoders.bean(Relation.class));
}
public static <R> Dataset<R> readPath(
final SparkSession spark,
final String inputPath,
@ -67,6 +78,7 @@ public class ClusterUtils {
.map(o -> ClusterUtils.incrementAccumulator(o, acc), Encoders.bean(clazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(path);
}

View File

@ -74,7 +74,7 @@ public class ConversionUtils {
}
final OaBrokerRelatedDataset res = new OaBrokerRelatedDataset();
res.setOpenaireId(d.getId());
res.setOpenaireId(cleanOpenaireId(d.getId()));
res.setOriginalId(first(d.getOriginalId()));
res.setTitle(structPropValue(d.getTitle()));
res.setPids(mappedList(d.getPid(), ConversionUtils::oafPidToBrokerPid));
@ -89,7 +89,7 @@ public class ConversionUtils {
}
final OaBrokerRelatedPublication res = new OaBrokerRelatedPublication();
res.setOpenaireId(p.getId());
res.setOpenaireId(cleanOpenaireId(p.getId()));
res.setOriginalId(first(p.getOriginalId()));
res.setTitle(structPropValue(p.getTitle()));
res.setPids(mappedList(p.getPid(), ConversionUtils::oafPidToBrokerPid));
@ -106,7 +106,7 @@ public class ConversionUtils {
final OaBrokerMainEntity res = new OaBrokerMainEntity();
res.setOpenaireId(result.getId());
res.setOpenaireId(cleanOpenaireId(result.getId()));
res.setOriginalId(first(result.getOriginalId()));
res.setTypology(classId(result.getResulttype()));
res.setTitles(structPropList(result.getTitle()));
@ -129,6 +129,10 @@ public class ConversionUtils {
return res;
}
public static String cleanOpenaireId(final String id) {
return id.contains("|") ? StringUtils.substringAfter(id, "|") : id;
}
private static OaBrokerAuthor oafAuthorToBrokerAuthor(final Author author) {
if (author == null) {
return null;
@ -188,7 +192,7 @@ public class ConversionUtils {
}
final OaBrokerProject res = new OaBrokerProject();
res.setOpenaireId(p.getId());
res.setOpenaireId(cleanOpenaireId(p.getId()));
res.setTitle(fieldValue(p.getTitle()));
res.setAcronym(fieldValue(p.getAcronym()));
res.setCode(fieldValue(p.getCode()));
@ -214,7 +218,7 @@ public class ConversionUtils {
}
final OaBrokerRelatedSoftware res = new OaBrokerRelatedSoftware();
res.setOpenaireId(sw.getId());
res.setOpenaireId(cleanOpenaireId(sw.getId()));
res.setName(structPropValue(sw.getTitle()));
res.setDescription(fieldValue(sw.getDescription()));
res.setRepository(fieldValue(sw.getCodeRepositoryUrl()));
@ -230,7 +234,7 @@ public class ConversionUtils {
final OaBrokerRelatedDatasource res = new OaBrokerRelatedDatasource();
res.setName(StringUtils.defaultIfBlank(fieldValue(ds.getOfficialname()), fieldValue(ds.getEnglishname())));
res.setOpenaireId(ds.getId());
res.setOpenaireId(cleanOpenaireId(ds.getId()));
res.setType(classId(ds.getDatasourcetype()));
return res;
}

View File

@ -59,9 +59,18 @@ public class DatasourceRelationsAccumulator implements Serializable {
final DatasourceRelationsAccumulator res = new DatasourceRelationsAccumulator();
collectedFromSet
.stream()
.map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.COLLECTED_FROM_REL))
.map(
s -> new Tuple3<>(ConversionUtils.cleanOpenaireId(r.getId()), ConversionUtils.cleanOpenaireId(s),
BrokerConstants.COLLECTED_FROM_REL))
.forEach(res::addTuple);
hostedBySet.stream().map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.HOSTED_BY_REL)).forEach(res::addTuple);
hostedBySet
.stream()
.map(
s -> new Tuple3<>(ConversionUtils.cleanOpenaireId(r.getId()), ConversionUtils.cleanOpenaireId(s),
BrokerConstants.HOSTED_BY_REL))
.forEach(res::addTuple);
return res;
}

View File

@ -76,6 +76,7 @@ public class EventFinder {
final Set<String> dsIdWhitelist,
final Set<String> dsIdBlacklist,
final Set<String> dsTypeWhitelist,
final Set<String> topicWhitelist,
final Map<String, LongAccumulator> accumulators) {
final List<UpdateInfo<?>> list = new ArrayList<>();
@ -84,7 +85,13 @@ public class EventFinder {
for (final OaBrokerRelatedDatasource targetDs : target.getDatasources()) {
if (verifyTarget(targetDs, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) {
for (final UpdateMatcher<?> matcher : matchers) {
list.addAll(matcher.searchUpdatesForRecord(target, targetDs, results.getData(), accumulators));
for (final UpdateInfo<?> info : matcher
.searchUpdatesForRecord(target, targetDs, results.getData(), accumulators)) {
if (topicWhitelist == null || topicWhitelist.isEmpty()
|| topicWhitelist.contains(info.getTopic().getPath())) {
list.add(info);
}
}
}
}
}

View File

@ -0,0 +1,9 @@
[
{
"paramName": "o",
"paramLongName": "outputDir",
"paramDescription": "the path where the data are stored",
"paramRequired": true
}
]

View File

@ -7,7 +7,7 @@
},
{
"paramName": "o",
"paramLongName": "workingPath",
"paramLongName": "workingDir",
"paramDescription": "the path where the temporary data will be stored",
"paramRequired": true
}

View File

@ -6,7 +6,7 @@
<description>the path where the graph is stored</description>
</property>
<property>
<name>workingPath</name>
<name>outputDir</name>
<description>the path where the the generated data will be stored</description>
</property>
<property>
@ -24,6 +24,11 @@
<value>-</value>
<description>a black list (comma separeted, - for empty list) of datasource ids</description>
</property>
<property>
<name>topicWhitelist</name>
<value>*</value>
<description>a white list (comma separeted, * for all) of topics</description>
</property>
<property>
<name>esEventIndexName</name>
<description>the elasticsearch index name for events</description>
@ -36,6 +41,26 @@
<name>esIndexHost</name>
<description>the elasticsearch host</description>
</property>
<property>
<name>esBatchWriteRetryCount</name>
<value>8</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esBatchWriteRetryWait</name>
<value>60s</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esBatchSizeEntries</name>
<value>200</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esNodesWanOnly</name>
<value>true</value>
<description>an ES configuration property</description>
</property>
<property>
<name>maxIndexedEventsForDsAndTopic</name>
<description>the max number of events for each couple (ds/topic)</description>
@ -111,15 +136,25 @@
</configuration>
</global>
<start to="ensure_working_path"/>
<start to="resume_from"/>
<decision name="resume_from">
<switch>
<case to="ensure_output_dir">${wf:conf('resumeFrom') eq 'ensure_output_dir'}</case>
<case to="index_event_subset">${wf:conf('resumeFrom') eq 'index_event_subset'}</case>
<case to="stats">${wf:conf('resumeFrom') eq 'stats'}</case>
<case to="index_notifications">${wf:conf('resumeFrom') eq 'index_notifications'}</case>
<default to="ensure_output_dir"/>
</switch>
</decision>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ensure_working_path">
<action name="ensure_output_dir">
<fs>
<mkdir path='${workingPath}'/>
<mkdir path='${outputDir}'/>
</fs>
<ok to="start_entities_and_rels"/>
<error to="Kill"/>
@ -152,7 +187,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -176,7 +211,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -201,7 +236,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -225,7 +260,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -249,7 +284,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -273,7 +308,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -299,7 +334,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="join_entities_step1"/>
<error to="Kill"/>
@ -323,7 +358,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="join_entities_step2"/>
<error to="Kill"/>
@ -347,7 +382,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="join_entities_step3"/>
<error to="Kill"/>
@ -371,7 +406,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="join_entities_step4"/>
<error to="Kill"/>
@ -395,7 +430,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="prepare_groups"/>
<error to="Kill"/>
@ -419,7 +454,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="generate_events"/>
<error to="Kill"/>
@ -442,10 +477,12 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--datasourceIdWhitelist</arg><arg>${datasourceIdWhitelist}</arg>
<arg>--datasourceTypeWhitelist</arg><arg>${datasourceTypeWhitelist}</arg>
<arg>--datasourceIdBlacklist</arg><arg>${datasourceIdBlacklist}</arg>
<arg>--topicWhitelist</arg><arg>${topicWhitelist}</arg>
</spark>
<ok to="index_event_subset"/>
<error to="Kill"/>
@ -468,38 +505,16 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--index</arg><arg>${esEventIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
<arg>--esBatchWriteRetryCount</arg><arg>${esBatchWriteRetryCount}</arg>
<arg>--esBatchWriteRetryWait</arg><arg>${esBatchWriteRetryWait}</arg>
<arg>--esBatchSizeEntries</arg><arg>${esBatchSizeEntries}</arg>
<arg>--esNodesWanOnly</arg><arg>${esNodesWanOnly}</arg>
<arg>--maxEventsForTopic</arg><arg>${maxIndexedEventsForDsAndTopic}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
<ok to="index_notifications"/>
<error to="Kill"/>
</action>
<action name="index_notifications">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>IndexNotificationsOnESJob</name>
<class>eu.dnetlib.dhp.broker.oa.IndexNotificationsJob</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.dynamicAllocation.maxExecutors="8"
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--index</arg><arg>${esNotificationsIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
<ok to="stats"/>
<error to="Kill"/>
</action>
@ -521,12 +536,42 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--dbUrl</arg><arg>${brokerDbUrl}</arg>
<arg>--dbUser</arg><arg>${brokerDbUser}</arg>
<arg>--dbPassword</arg><arg>${brokerDbPassword}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
<ok to="index_notifications"/>
<error to="Kill"/>
</action>
<action name="index_notifications">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>IndexNotificationsOnESJob</name>
<class>eu.dnetlib.dhp.broker.oa.IndexNotificationsJob</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.dynamicAllocation.maxExecutors="8"
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--index</arg><arg>${esNotificationsIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
<arg>--esBatchWriteRetryCount</arg><arg>${esBatchWriteRetryCount}</arg>
<arg>--esBatchWriteRetryWait</arg><arg>${esBatchWriteRetryWait}</arg>
<arg>--esBatchSizeEntries</arg><arg>${esBatchSizeEntries}</arg>
<arg>--esNodesWanOnly</arg><arg>${esNodesWanOnly}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>

View File

@ -1,7 +1,13 @@
[
{
"paramName": "wp",
"paramLongName": "workingDir",
"paramDescription": "the path where the temporary data are stored",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "workingPath",
"paramLongName": "outputDir",
"paramDescription": "the path where the generated events will be stored",
"paramRequired": true
},
@ -22,5 +28,11 @@
"paramLongName": "datasourceIdBlacklist",
"paramDescription": "a black list (comma separeted, - for empty list) of datasource ids",
"paramRequired": true
},
{
"paramName": "topicWhitelist",
"paramLongName": "topicWhitelist",
"paramDescription": "a white list (comma separeted, * for all) of topics",
"paramRequired": true
}
]

View File

@ -1,8 +1,8 @@
[
{
"paramName": "o",
"paramLongName": "workingPath",
"paramDescription": "the workinh path",
"paramLongName": "outputDir",
"paramDescription": "the data path",
"paramRequired": true
},
{
@ -16,5 +16,29 @@
"paramLongName": "esHost",
"paramDescription": "the ES host",
"paramRequired": true
},
{
"paramName": "esBatchWriteRetryCount",
"paramLongName": "esBatchWriteRetryCount",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esBatchWriteRetryWait",
"paramLongName": "esBatchWriteRetryWait",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esBatchSizeEntries",
"paramLongName": "esBatchSizeEntries",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esNodesWanOnly",
"paramLongName": "esNodesWanOnly",
"paramDescription": "an ES configuration property",
"paramRequired": true
}
]

View File

@ -1,8 +1,8 @@
[
{
"paramName": "o",
"paramLongName": "workingPath",
"paramDescription": "the workinh path",
"paramLongName": "outputDir",
"paramDescription": "the path where the generated data are stored",
"paramRequired": true
},
{
@ -17,6 +17,30 @@
"paramDescription": "the ES host",
"paramRequired": true
},
{
"paramName": "esBatchWriteRetryCount",
"paramLongName": "esBatchWriteRetryCount",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esBatchWriteRetryWait",
"paramLongName": "esBatchWriteRetryWait",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esBatchSizeEntries",
"paramLongName": "esBatchSizeEntries",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esNodesWanOnly",
"paramLongName": "esNodesWanOnly",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "n",
"paramLongName": "maxEventsForTopic",

View File

@ -1,8 +1,8 @@
[
{
"paramName": "o",
"paramLongName": "workingPath",
"paramDescription": "the workinh path",
"paramLongName": "outputDir",
"paramDescription": "the dir that contains the events folder",
"paramRequired": true
},
{
@ -17,6 +17,30 @@
"paramDescription": "the ES host",
"paramRequired": true
},
{
"paramName": "esBatchWriteRetryCount",
"paramLongName": "esBatchWriteRetryCount",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esBatchWriteRetryWait",
"paramLongName": "esBatchWriteRetryWait",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esBatchSizeEntries",
"paramLongName": "esBatchSizeEntries",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "esNodesWanOnly",
"paramLongName": "esNodesWanOnly",
"paramDescription": "an ES configuration property",
"paramRequired": true
},
{
"paramName": "broker",
"paramLongName": "brokerApiBaseUrl",

View File

@ -6,8 +6,8 @@
<description>the path where the graph is stored</description>
</property>
<property>
<name>workingPath</name>
<description>the path where the the generated data will be stored</description>
<name>outputDir</name>
<description>the path where the the generated data are stored</description>
</property>
<property>
<name>datasourceIdWhitelist</name>
@ -36,6 +36,26 @@
<name>esIndexHost</name>
<description>the elasticsearch host</description>
</property>
<property>
<name>esBatchWriteRetryCount</name>
<value>8</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esBatchWriteRetryWait</name>
<value>60s</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esBatchSizeEntries</name>
<value>200</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esNodesWanOnly</name>
<value>true</value>
<description>an ES configuration property</description>
</property>
<property>
<name>maxIndexedEventsForDsAndTopic</name>
<description>the max number of events for each couple (ds/topic)</description>
@ -122,9 +142,13 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--index</arg><arg>${esNotificationsIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
<arg>--esBatchWriteRetryCount</arg><arg>${esBatchWriteRetryCount}</arg>
<arg>--esBatchWriteRetryWait</arg><arg>${esBatchWriteRetryWait}</arg>
<arg>--esBatchSizeEntries</arg><arg>${esBatchSizeEntries}</arg>
<arg>--esNodesWanOnly</arg><arg>${esNodesWanOnly}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
<ok to="End"/>

View File

@ -1,8 +1,8 @@
[
{
"paramName": "o",
"paramLongName": "workingPath",
"paramDescription": "the path where the temporary data will be stored",
"paramLongName": "outputDir",
"paramDescription": "the path where the data will be stored",
"paramRequired": true
},
{

View File

@ -6,7 +6,7 @@
<description>the opendoar IDs whitelist (comma separated)</description>
</property>
<property>
<name>workingPath</name>
<name>outputDir</name>
<description>the path where the the generated data will be stored</description>
</property>
<property>
@ -87,7 +87,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--opendoarIds</arg><arg>${opendoarIds}</arg>
</spark>
<ok to="End"/>

View File

@ -0,0 +1,18 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

View File

@ -0,0 +1,140 @@
<workflow-app name="reindex_events" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>outputDir</name>
<description>the path where the the generated data will be stored</description>
</property>
<property>
<name>esEventIndexName</name>
<description>the elasticsearch index name for events</description>
</property>
<property>
<name>esIndexHost</name>
<description>the elasticsearch host</description>
</property>
<property>
<name>esBatchWriteRetryCount</name>
<value>8</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esBatchWriteRetryWait</name>
<value>60s</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esBatchSizeEntries</name>
<value>200</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esNodesWanOnly</name>
<value>true</value>
<description>an ES configuration property</description>
</property>
<property>
<name>maxIndexedEventsForDsAndTopic</name>
<description>the max number of events for each couple (ds/topic)</description>
</property>
<property>
<name>brokerApiBaseUrl</name>
<description>the url of the broker service api</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="index_event_subset"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="index_event_subset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>IndexEventSubsetOnESJob</name>
<class>eu.dnetlib.dhp.broker.oa.IndexEventSubsetJob</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.dynamicAllocation.maxExecutors="8"
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--index</arg><arg>${esEventIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
<arg>--esBatchWriteRetryCount</arg><arg>${esBatchWriteRetryCount}</arg>
<arg>--esBatchWriteRetryWait</arg><arg>${esBatchWriteRetryWait}</arg>
<arg>--esBatchSizeEntries</arg><arg>${esBatchSizeEntries}</arg>
<arg>--esNodesWanOnly</arg><arg>${esNodesWanOnly}</arg>
<arg>--maxEventsForTopic</arg><arg>${maxIndexedEventsForDsAndTopic}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

View File

@ -0,0 +1,18 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

View File

@ -0,0 +1,114 @@
<workflow-app name="create broker events" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>outputDir</name>
<description>the path where the the generated data will be stored</description>
</property>
<property>
<name>brokerApiBaseUrl</name>
<description>the url of the broker service api</description>
</property>
<property>
<name>brokerDbUrl</name>
<description>the url of the broker database</description>
</property>
<property>
<name>brokerDbUser</name>
<description>the user of the broker database</description>
</property>
<property>
<name>brokerDbPassword</name>
<description>the password of the broker database</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="stats"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="stats">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>GenerateStatsJob</name>
<class>eu.dnetlib.dhp.broker.oa.GenerateStatsJob</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--dbUrl</arg><arg>${brokerDbUrl}</arg>
<arg>--dbUser</arg><arg>${brokerDbUser}</arg>
<arg>--dbPassword</arg><arg>${brokerDbPassword}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

View File

@ -1,8 +1,8 @@
[
{
"paramName": "wp",
"paramLongName": "workingPath",
"paramDescription": "the working path",
"paramName": "o",
"paramLongName": "outputDir",
"paramDescription": "the path where generated data are stored",
"paramRequired": true
},
{

View File

@ -7,7 +7,6 @@ import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.PairFunction;
@ -16,8 +15,8 @@ import org.apache.spark.rdd.RDD;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.codehaus.jackson.map.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.hash.Hashing;
import eu.dnetlib.dedup.graph.ConnectedComponent;

View File

@ -10,7 +10,8 @@ import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.codehaus.jackson.map.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Oaf;

View File

@ -4,14 +4,13 @@ import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Organization, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import org.codehaus.jackson.map.ObjectMapper
import com.fasterxml.jackson.databind.ObjectMapper
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import scala.io.Source
case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {}
@ -19,23 +18,18 @@ case class HostedByItemType(id: String, officialname: String, issn: String, eiss
case class DoiBoostAffiliation(PaperId:Long, AffiliationId:Long, GridId:Option[String], OfficialPage:Option[String], DisplayName:Option[String]){}
object DoiBoostMappingUtil {
def getUnknownCountry(): Qualifier = {
createQualifier("UNKNOWN","UNKNOWN","dnet:countries","dnet:countries")
}
def generateMAGAffiliationId(affId: String): String = {
s"20|microsoft___$SEPARATOR${DHPUtils.md5(affId)}"
}
val logger: Logger = LoggerFactory.getLogger(getClass)
//STATIC STRING
val MAG = "microsoft"
val MAG_NAME = "Microsoft Academic Graph"
val ORCID = "ORCID"
val ORCID = "orcid"
val ORCID_PENDING = "orcid_pending"
val CROSSREF = "Crossref"
val UNPAYWALL = "UnpayWall"
val GRID_AC = "grid.ac"

View File

@ -39,33 +39,38 @@ object SparkGenerateDOIBoostActionSet {
val dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath")
val dbOrganizationPath = parser.get("dbOrganizationPath")
val workingDirPath = parser.get("targetPath")
val sequenceFilePath = parser.get("sFilePath")
spark.read.load(dbDatasetPath).as[OafDataset]
val asDataset = spark.read.load(dbDatasetPath).as[OafDataset]
.map(d =>DoiBoostMappingUtil.fixResult(d))
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Overwrite).save(s"$workingDirPath/actionSet")
// .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/actionSet")
spark.read.load(dbPublicationPath).as[Publication]
val asPublication =spark.read.load(dbPublicationPath).as[Publication]
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
spark.read.load(dbOrganizationPath).as[Organization]
val asOrganization = spark.read.load(dbOrganizationPath).as[Organization]
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
spark.read.load(crossRefRelation).as[Relation]
val asCRelation = spark.read.load(crossRefRelation).as[Relation]
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
spark.read.load(dbaffiliationRelationPath).as[Relation]
val asRelAffiliation = spark.read.load(dbaffiliationRelationPath).as[Relation]
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
// .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
val d: Dataset[(String, String)] =spark.read.load(s"$workingDirPath/actionSet").as[(String,String)]
d.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingDirPath/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
val d: Dataset[(String, String)] = asDataset.union(asPublication).union(asOrganization).union(asCRelation).union(asRelAffiliation)
// spark.read.load(s"$workingDirPath/actionSet").as[(String,String)]
d.rdd.repartition(6000).map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$sequenceFilePath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])

View File

@ -2,6 +2,7 @@ package eu.dnetlib.doiboost
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.oa.merge.AuthorMerger
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.doiboost.mag.ConversionUtil
import org.apache.commons.io.IOUtils
@ -30,7 +31,7 @@ object SparkGenerateDoiBoost {
import spark.implicits._
val hostedByMapPath = parser.get("hostedByMapPath")
val workingDirPath = parser.get("workingDirPath")
val workingDirPath = parser.get("workingPath")
implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
@ -132,7 +133,7 @@ object SparkGenerateDoiBoost {
o.setLegalname(DoiBoostMappingUtil.asField(affiliation.DisplayName.get))
if (affiliation.OfficialPage.isDefined)
o.setWebsiteurl(DoiBoostMappingUtil.asField(affiliation.OfficialPage.get))
o.setCountry(DoiBoostMappingUtil.getUnknownCountry())
o.setCountry(ModelConstants.UNKNOWN_COUNTRY)
o
}
else

View File

@ -206,7 +206,7 @@ case object Crossref2Oaf {
a.setSurname(family)
a.setFullname(s"$given $family")
if (StringUtils.isNotBlank(orcid))
a.setPid(List(createSP(orcid, ORCID, PID_TYPES, generateDataInfo())).asJava)
a.setPid(List(createSP(orcid, ORCID_PENDING, PID_TYPES, generateDataInfo())).asJava)
a
}

View File

@ -2,18 +2,16 @@
package eu.dnetlib.doiboost.crossref;
import java.io.ByteArrayOutputStream;
import java.util.Optional;
import java.util.zip.Inflater;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
@ -30,34 +28,45 @@ public class CrossrefImporter {
parser.parseArgument(args);
final String hdfsuri = parser.get("namenode");
System.out.println("HDFS URI" + hdfsuri);
Path hdfswritepath = new Path(parser.get("targetPath"));
System.out.println("TargetPath: " + hdfsuri);
final String namenode = parser.get("namenode");
System.out.println("namenode: " + namenode);
final Long timestamp = StringUtils.isNotBlank(parser.get("timestamp"))
? Long.parseLong(parser.get("timestamp"))
: -1;
Path targetPath = new Path(parser.get("targetPath"));
System.out.println("targetPath: " + targetPath);
if (timestamp > 0)
System.out.println("Timestamp added " + timestamp);
final Long timestamp = Optional
.ofNullable(parser.get("timestamp"))
.map(s -> {
try {
return Long.parseLong(s);
} catch (NumberFormatException e) {
return -1L;
}
})
.orElse(-1L);
System.out.println("timestamp: " + timestamp);
final String esServer = parser.get("esServer");
System.out.println("esServer: " + esServer);
final String esIndex = parser.get("esIndex");
System.out.println("esIndex: " + esIndex);
// ====== Init HDFS File System Object
Configuration conf = new Configuration();
// Set FileSystem URI
conf.set("fs.defaultFS", hdfsuri);
conf.set("fs.defaultFS", namenode);
// Because of Maven
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
ESClient client = timestamp > 0
? new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref", timestamp)
: new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref");
// "ip-90-147-167-25.ct1.garrservices.it", "crossref"
final ESClient client = new ESClient(esServer, esIndex, timestamp);
try (SequenceFile.Writer writer = SequenceFile
.createWriter(
conf,
SequenceFile.Writer.file(hdfswritepath),
SequenceFile.Writer.file(targetPath),
SequenceFile.Writer.keyClass(IntWritable.class),
SequenceFile.Writer.valueClass(Text.class))) {
@ -74,8 +83,7 @@ public class CrossrefImporter {
end = System.currentTimeMillis();
final float time = (end - start) / 1000.0F;
System.out
.println(
String.format("Imported %d records last 100000 imported in %f seconds", i, time));
.println(String.format("Imported %s records last 100000 imported in %s seconds", i, time));
start = System.currentTimeMillis();
}
}

View File

@ -1,11 +1,11 @@
package eu.dnetlib.doiboost.crossref;
import java.io.IOException;
import java.util.Iterator;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.http.HttpHeaders;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.StringEntity;
@ -17,13 +17,17 @@ import org.slf4j.LoggerFactory;
import com.jayway.jsonpath.JsonPath;
public class ESClient implements Iterator<String> {
private static final Logger logger = LoggerFactory.getLogger(ESClient.class);
static final String blobPath = "$.hits[*].hits[*]._source.blob";
static final String scrollIdPath = "$._scroll_id";
static final String JSON_NO_TS = "{\"size\":1000}";
static final String JSON_WITH_TS = "{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}";
static final String JSON_SCROLL = "{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}";
private static final String BLOB_PATH = "$.hits.hits[*]._source.blob";
private static final String SCROLL_ID_PATH = "$._scroll_id";
private static final String JSON_NO_TS = "{\"size\":1000}";
private static final String JSON_WITH_TS = "{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}";
private static final String JSON_SCROLL = "{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}";
public static final String APPLICATION_JSON = "application/json";
public static final String ES_SEARCH_URL = "http://%s:9200/%s/_search?scroll=1m";
public static final String ES_SCROLL_URL = "http://%s:9200/_search/scroll";
private final String scrollId;
@ -31,47 +35,30 @@ public class ESClient implements Iterator<String> {
private final String esHost;
public ESClient(final String esHost, final String esIndex) throws IOException {
public ESClient(final String esHost, final String esIndex, final long timestamp) {
this.esHost = esHost;
final String body = getResponse(
String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), JSON_NO_TS);
scrollId = getJPathString(scrollIdPath, body);
buffer = getBlobs(body);
}
public ESClient(final String esHost, final String esIndex, final long timestamp)
throws IOException {
this.esHost = esHost;
final String body = getResponse(
String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex),
String.format(JSON_WITH_TS, timestamp));
scrollId = getJPathString(scrollIdPath, body);
final String body = timestamp > 0
? getResponse(String.format(ES_SEARCH_URL, esHost, esIndex), String.format(JSON_WITH_TS, timestamp))
: getResponse(String.format(ES_SEARCH_URL, esHost, esIndex), JSON_NO_TS);
scrollId = getJPathString(SCROLL_ID_PATH, body);
buffer = getBlobs(body);
}
private String getResponse(final String url, final String json) {
CloseableHttpClient client = HttpClients.createDefault();
try {
try (CloseableHttpClient client = HttpClients.createDefault()) {
HttpPost httpPost = new HttpPost(url);
if (json != null) {
StringEntity entity = new StringEntity(json);
httpPost.setEntity(entity);
httpPost.setHeader("Accept", "application/json");
httpPost.setHeader("Content-type", "application/json");
httpPost.setHeader(HttpHeaders.ACCEPT, APPLICATION_JSON);
httpPost.setHeader(HttpHeaders.CONTENT_TYPE, APPLICATION_JSON);
}
try (CloseableHttpResponse response = client.execute(httpPost)) {
return IOUtils.toString(response.getEntity().getContent());
}
CloseableHttpResponse response = client.execute(httpPost);
return IOUtils.toString(response.getEntity().getContent());
} catch (Throwable e) {
throw new RuntimeException("Error on executing request ", e);
} finally {
try {
client.close();
} catch (IOException e) {
throw new RuntimeException("Unable to close client ", e);
}
}
}
@ -87,7 +74,7 @@ public class ESClient implements Iterator<String> {
}
private List<String> getBlobs(final String body) {
final List<String> res = JsonPath.read(body, "$.hits.hits[*]._source.blob");
final List<String> res = JsonPath.read(body, BLOB_PATH);
return res;
}
@ -102,11 +89,11 @@ public class ESClient implements Iterator<String> {
if (buffer.isEmpty()) {
final String json_param = String.format(JSON_SCROLL, scrollId);
final String body = getResponse(String.format("http://%s:9200/_search/scroll", esHost), json_param);
final String body = getResponse(String.format(ES_SCROLL_URL, esHost), json_param);
try {
buffer = getBlobs(body);
} catch (Throwable e) {
logger.error("Error on get next page: body:" + body);
System.out.println("Error on get next page: body:" + body);
}
}
return nextItem;

View File

@ -11,7 +11,7 @@ import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
object SparkPreProcessMAG {
object SparkProcessMAG {
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(getClass)

View File

@ -1,11 +1,11 @@
package eu.dnetlib.doiboost.orcid
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Publication}
import eu.dnetlib.dhp.schema.orcid.OrcidDOI
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{ORCID, PID_TYPES, createSP, generateDataInfo, generateIdentifier}
import org.apache.commons.lang.StringUtils
import org.codehaus.jackson.map.ObjectMapper
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
@ -18,7 +18,7 @@ case class ORCIDItem(oid:String,name:String,surname:String,creditName:String,err
case class ORCIDElement(doi:String, authors:List[ORCIDItem]) {}
object ORCIDToOAF {
val logger: Logger = LoggerFactory.getLogger(ORCIDToOAF.getClass)
val mapper = new ObjectMapper
val mapper = new ObjectMapper()
def isJsonValid(inputStr: String): Boolean = {
import java.io.IOException

View File

@ -3,10 +3,8 @@ package eu.dnetlib.doiboost.orcid;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.List;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
@ -18,11 +16,9 @@ import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.Function;
import org.apache.spark.util.LongAccumulator;
import org.mortbay.log.Log;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -36,7 +32,7 @@ public class SparkDownloadOrcidAuthors {
static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
static final String lastUpdate = "2020-09-29 00:00:00";
public static void main(String[] args) throws IOException, Exception {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
@ -51,12 +47,12 @@ public class SparkDownloadOrcidAuthors {
.orElse(Boolean.TRUE);
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
logger.info("workingPath: ", workingPath);
logger.info("workingPath: {}", workingPath);
final String outputPath = parser.get("outputPath");
logger.info("outputPath: ", outputPath);
logger.info("outputPath: {}", outputPath);
final String token = parser.get("token");
final String lambdaFileName = parser.get("lambdaFileName");
logger.info("lambdaFileName: ", lambdaFileName);
logger.info("lambdaFileName: {}", lambdaFileName);
SparkConf conf = new SparkConf();
runWithSparkSession(
@ -171,8 +167,8 @@ public class SparkDownloadOrcidAuthors {
}
private static boolean isModified(String orcidId, String modifiedDate) {
Date modifiedDateDt = null;
Date lastUpdateDt = null;
Date modifiedDateDt;
Date lastUpdateDt;
try {
if (modifiedDate.length() != 19) {
modifiedDate = modifiedDate.substring(0, 19);

View File

@ -5,5 +5,6 @@
{"paramName": "cr", "paramLongName":"crossRefRelation", "paramDescription": "the UnpayWall Publication Path", "paramRequired": true},
{"paramName": "da", "paramLongName":"dbaffiliationRelationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true},
{"paramName": "do", "paramLongName":"dbOrganizationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true},
{"paramName": "w", "paramLongName":"targetPath", "paramDescription": "the Working Path", "paramRequired": true}
{"paramName": "w", "paramLongName":"targetPath", "paramDescription": "the Working Path", "paramRequired": true},
{"paramName": "sp", "paramLongName":"sFilePath", "paramDescription": "the Sequence file Path", "paramRequired": true}
]

View File

@ -3,5 +3,5 @@
{"paramName": "hb", "paramLongName":"hostedByMapPath", "paramDescription": "the hosted By Map Path", "paramRequired": true},
{"paramName": "ap", "paramLongName":"affiliationPath", "paramDescription": "the Affliation Path", "paramRequired": true},
{"paramName": "pa", "paramLongName":"paperAffiliationPath", "paramDescription": "the paperAffiliation Path", "paramRequired": true},
{"paramName": "w", "paramLongName":"workingDirPath", "paramDescription": "the Working Path", "paramRequired": true}
{"paramName": "w", "paramLongName":"workingPath", "paramDescription": "the Working Path", "paramRequired": true}
]

View File

@ -1,5 +1,7 @@
[
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the sequencial file to write", "paramRequired": true},
{"paramName":"n", "paramLongName":"namenode", "paramDescription": "the hive metastore uris", "paramRequired": true},
{"paramName":"ts", "paramLongName":"timestamp", "paramDescription": "timestamp", "paramRequired": false}
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the sequencial file to write", "paramRequired": true},
{"paramName":"n", "paramLongName":"namenode", "paramDescription": "the hive metastore uris", "paramRequired": true},
{"paramName":"ts", "paramLongName":"timestamp", "paramDescription": "timestamp", "paramRequired": false},
{"paramName":"ess", "paramLongName":"esServer", "paramDescription": "elasticsearch server url", "paramRequired": true},
{"paramName":"esi", "paramLongName":"esIndex", "paramDescription": "elasticsearch index name", "paramRequired": true}
]

View File

@ -15,6 +15,10 @@
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
@ -23,36 +27,16 @@
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
<property>
<name>sparkExecutorNumber</name>
<value>4</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>sparkDriverMemory</name>
<value>15G</value>
<name>spark2ExtraListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
</property>
<property>
<name>sparkExecutorMemory</name>
<value>6G</value>
</property>
<property>
<name>sparkExecutorCores</name>
<value>1</value>
<name>spark2SqlQueryExecutionListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
</property>
</configuration>

View File

@ -0,0 +1,335 @@
<workflow-app name="Generate DOIBoost ActionSet" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorIntersectionMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<!-- Itersection Parameters -->
<property>
<name>workingPath</name>
<description>the working Path</description>
</property>
<property>
<name>hostedByMapPath</name>
<description>the hostedByMap Path</description>
</property>
<property>
<name>outputPath</name>
<description>the Path of the sequence file action set</description>
</property>
<!-- Crossref Parameters -->
<property>
<name>inputPathCrossref</name>
<description>the Crossref input path</description>
</property>
<property>
<name>crossrefTimestamp</name>
<description>Timestamp for the Crossref incremental Harvesting</description>
</property>
<property>
<name>esServer</name>
<description>elasticsearch server url for the Crossref Harvesting</description>
</property>
<property>
<name>esIndex</name>
<description>elasticsearch index name for the Crossref Harvesting</description>
</property>
<!-- MAG Parameters -->
<property>
<name>inputPathMAG</name>
<description>the MAG working path</description>
</property>
<!-- UnpayWall Parameters -->
<property>
<name>inputPathUnpayWall</name>
<description>the UnpayWall working path</description>
</property>
<!-- ORCID Parameters -->
<property>
<name>inputPathOrcid</name>
<description>the ORCID working path</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="resume_from"/>
<decision name="resume_from">
<switch>
<case to="ConvertCrossrefToOAF">${wf:conf('resumeFrom') eq 'ConvertCrossrefToOAF'}</case>
<case to="ResetMagWorkingPath">${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'}</case>
<case to="ProcessMAG">${wf:conf('resumeFrom') eq 'PreprocessMag'}</case>
<case to="ProcessUW">${wf:conf('resumeFrom') eq 'PreprocessUW'}</case>
<case to="ProcessORCID">${wf:conf('resumeFrom') eq 'PreprocessORCID'}</case>
<case to="CreateDOIBoost">${wf:conf('resumeFrom') eq 'CreateDOIBoost'}</case>
<case to="GenerateActionSet">${wf:conf('resumeFrom') eq 'GenerateActionSet'}</case>
<default to="ImportCrossRef"/>
</switch>
</decision>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ImportCrossRef">
<java>
<main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>
<arg>--targetPath</arg><arg>${inputPathCrossref}/index_update</arg>
<arg>--namenode</arg><arg>${nameNode}</arg>
<arg>--esServer</arg><arg>${esServer}</arg>
<arg>--esIndex</arg><arg>${esIndex}</arg>
<arg>--timestamp</arg><arg>${crossrefTimestamp}</arg>
</java>
<ok to="GenerateCrossrefDataset"/>
<error to="Kill"/>
</action>
<!-- CROSSREF SECTION -->
<action name="GenerateCrossrefDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>GenerateCrossrefDataset</name>
<class>eu.dnetlib.doiboost.crossref.CrossrefDataset</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--workingPath</arg><arg>${inputPathCrossref}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="RenameDataset"/>
<error to="Kill"/>
</action>
<action name="RenameDataset">
<fs>
<delete path="${inputPathCrossref}/crossref_ds"/>
<move source="${inputPathCrossref}/crossref_ds_updated"
target="${inputPathCrossref}/crossref_ds"/>
</fs>
<ok to="ConvertCrossrefToOAF"/>
<error to="Kill"/>
</action>
<action name="ConvertCrossrefToOAF">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ConvertCrossrefToOAF</name>
<class>eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
<arg>--targetPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="ResetMagWorkingPath"/>
<error to="Kill"/>
</action>
<!-- MAG SECTION -->
<action name="ResetMagWorkingPath">
<fs>
<delete path="${inputPathMAG}/dataset"/>
<delete path="${inputPathMAG}/process"/>
<delete path="${inputPathMAG}/dataset"/>
</fs>
<ok to="ConvertMagToDataset"/>
<error to="Kill"/>
</action>
<action name="ConvertMagToDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert Mag to Dataset</name>
<class>eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${inputPathMAG}/input</arg>
<arg>--targetPath</arg><arg>${inputPathMAG}/dataset</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="ProcessMAG"/>
<error to="Kill"/>
</action>
<action name="ProcessMAG">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert Mag to OAF Dataset</name>
<class>eu.dnetlib.doiboost.mag.SparkProcessMAG</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${inputPathMAG}/dataset</arg>
<arg>--workingPath</arg><arg>${inputPathMAG}/process</arg>
<arg>--targetPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="ProcessUW"/>
<error to="Kill"/>
</action>
<!-- UnpayWall SECTION -->
<action name="ProcessUW">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert UnpayWall to Dataset</name>
<class>eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${inputPathUnpayWall}/uw_extracted</arg>
<arg>--targetPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="ProcessORCID"/>
<error to="Kill"/>
</action>
<!-- ORCID SECTION -->
<action name="ProcessORCID">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert ORCID to Dataset</name>
<class>eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${inputPathOrcid}</arg>
<arg>--targetPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="CreateDOIBoost"/>
<error to="Kill"/>
</action>
<!-- INTERSECTION SECTION-->
<action name="CreateDOIBoost">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create DOIBoost Infospace</name>
<class>eu.dnetlib.doiboost.SparkGenerateDoiBoost</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorIntersectionMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
<arg>--affiliationPath</arg><arg>${inputPathMAG}/process/Affiliations</arg>
<arg>--paperAffiliationPath</arg><arg>${inputPathMAG}/process/PaperAuthorAffiliations</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="GenerateActionSet"/>
<error to="Kill"/>
</action>
<action name="GenerateActionSet">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Generate DOIBoost ActionSet</name>
<class>eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--dbPublicationPath</arg><arg>${workingPath}/doiBoostPublicationFiltered</arg>
<arg>--dbDatasetPath</arg><arg>${workingPath}/crossrefDataset</arg>
<arg>--crossRefRelation</arg><arg>${workingPath}/crossrefRelation</arg>
<arg>--dbaffiliationRelationPath</arg><arg>${workingPath}/doiBoostPublicationAffiliation</arg>
<arg>--dbOrganizationPath</arg><arg>${workingPath}/doiBoostOrganization</arg>
<arg>--targetPath</arg><arg>${workingPath}/actionDataSet</arg>
<arg>--sFilePath</arg><arg>${outputPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

View File

@ -1,9 +1,9 @@
package eu.dnetlib.doiboost.orcid
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF.getClass
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.codehaus.jackson.map.ObjectMapper
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.Test
import org.slf4j.{Logger, LoggerFactory}

View File

@ -104,7 +104,7 @@ public class PrepareResultOrcidAssociationStep1 {
+ " LATERAL VIEW EXPLODE (author) a AS MyT "
+ " LATERAL VIEW EXPLODE (MyT.pid) p AS MyP "
+ " WHERE lower(MyP.qualifier.classid) = '" + ModelConstants.ORCID + "' or "
+ " lower(MyP.qalifier.classid) = '" + ModelConstants.ORCID_PENDING + "') tmp "
+ " lower(MyP.qualifier.classid) = '" + ModelConstants.ORCID_PENDING + "') tmp "
+ " GROUP BY id) r_t "
+ " JOIN ("
+ " SELECT source, target "

View File

@ -108,7 +108,7 @@ public class SparkResultToCommunityFromOrganizationJob {
.stream()
.map(con -> con.getId())
.collect(Collectors.toList());
Result res = new Result();
R res = (R) ret.getClass().newInstance();
res.setId(ret.getId());
List<Context> propagatedContexts = new ArrayList<>();
for (String cId : communitySet) {

View File

@ -130,7 +130,7 @@ public class SparkResultToCommunityThroughSemRelJob {
})
.filter(Objects::nonNull)
.collect(Collectors.toList());
Result r = new Result();
R r = (R) ret.getClass().newInstance();
r.setId(ret.getId());
r.setContext(contextList);
ret.mergeFrom(r);

View File

@ -24,7 +24,6 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.orcidtoresultfromsemrel.OrcidPropagationJobTest;
import eu.dnetlib.dhp.schema.oaf.Dataset;
public class ResultToCommunityJobTest {
@ -66,7 +65,7 @@ public class ResultToCommunityJobTest {
}
@Test
public void test1() throws Exception {
public void testSparkResultToCommunityThroughSemRelJob() throws Exception {
SparkResultToCommunityThroughSemRelJob
.main(
new String[] {

View File

@ -23,7 +23,15 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.*;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.asString;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.dataInfo;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.field;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.journal;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listFields;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listKeyValues;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.qualifier;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.structuredProperty;
import java.io.Closeable;
import java.io.IOException;
@ -462,44 +470,48 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
return Arrays.asList(r);
} else {
final String validationDate = rs.getString("curation_date");
final String sourceId = createOpenaireId(rs.getString(SOURCE_TYPE), rs.getString("source_id"), false);
final String targetId = createOpenaireId(rs.getString(TARGET_TYPE), rs.getString("target_id"), false);
final Relation r1 = new Relation();
final Relation r2 = new Relation();
if (rs.getString(SOURCE_TYPE).equals("project")) {
r1.setCollectedfrom(collectedFrom);
r1.setRelType(RESULT_PROJECT);
r1.setSubRelType(OUTCOME);
r1.setRelClass(PRODUCES);
r2.setCollectedfrom(collectedFrom);
r2.setRelType(RESULT_PROJECT);
r2.setSubRelType(OUTCOME);
r2.setRelClass(IS_PRODUCED_BY);
} else {
r1.setCollectedfrom(collectedFrom);
r1.setRelType(RESULT_RESULT);
r1.setSubRelType(RELATIONSHIP);
r1.setRelClass(IS_RELATED_TO);
r2.setCollectedfrom(collectedFrom);
r2.setRelType(RESULT_RESULT);
r2.setSubRelType(RELATIONSHIP);
r2.setRelClass(IS_RELATED_TO);
}
r1.setValidated(true);
r1.setValidationDate(validationDate);
r1.setCollectedfrom(collectedFrom);
r1.setSource(sourceId);
r1.setTarget(targetId);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
r2.setValidationDate(validationDate);
r2.setValidated(true);
r2.setCollectedfrom(collectedFrom);
r2.setSource(targetId);
r2.setTarget(sourceId);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
if (rs.getString(SOURCE_TYPE).equals("project")) {
r1.setRelType(RESULT_PROJECT);
r1.setSubRelType(OUTCOME);
r1.setRelClass(PRODUCES);
r2.setRelType(RESULT_PROJECT);
r2.setSubRelType(OUTCOME);
r2.setRelClass(IS_PRODUCED_BY);
} else {
r1.setRelType(RESULT_RESULT);
r1.setSubRelType(RELATIONSHIP);
r1.setRelClass(IS_RELATED_TO);
r2.setRelType(RESULT_RESULT);
r2.setSubRelType(RELATIONSHIP);
r2.setRelClass(IS_RELATED_TO);
}
return Arrays.asList(r1, r2);
}

View File

@ -36,31 +36,34 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
final Node n = (Node) o;
final Author author = new Author();
final String fullname = n.valueOf("./datacite:creatorName");
author.setFullname(fullname);
final PacePerson pp = new PacePerson(fullname, false);
final String name = n.valueOf("./datacite:givenName");
if (StringUtils.isBlank(name) & pp.isAccurate()) {
author.setName(pp.getNormalisedFirstName());
} else {
author.setName(name);
}
final String surname = n.valueOf("./datacite:familyName");
if (StringUtils.isBlank(surname) & pp.isAccurate()) {
author.setSurname(pp.getNormalisedSurname());
} else {
author.setSurname(surname);
}
if (StringUtils.isNotBlank(fullname) || StringUtils.isNotBlank(name) || StringUtils.isNotBlank(surname)) {
author.setFullname(fullname);
if (StringUtils.isBlank(author.getFullname())) {
author.setFullname(String.format("%s, %s", author.getSurname(), author.getName()));
}
final PacePerson pp = new PacePerson(fullname, false);
author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info));
author.setPid(preparePids(n, info));
author.setRank(pos++);
res.add(author);
if (StringUtils.isBlank(name) & pp.isAccurate()) {
author.setName(pp.getNormalisedFirstName());
} else {
author.setName(name);
}
if (StringUtils.isBlank(surname) & pp.isAccurate()) {
author.setSurname(pp.getNormalisedSurname());
} else {
author.setSurname(surname);
}
if (StringUtils.isBlank(author.getFullname())) {
author.setFullname(String.format("%s, %s", author.getSurname(), author.getName()));
}
author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info));
author.setPid(preparePids(n, info));
author.setRank(pos++);
res.add(author);
}
}
return res;
}

View File

@ -11,7 +11,8 @@ import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.codehaus.jackson.map.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Oaf;

View File

@ -1 +1 @@
SELECT source_type, source_id, target_type, target_id, semantics FROM claim WHERE approved=TRUE;
SELECT source_type, source_id, target_type, target_id, semantics, curation_date::text FROM claim WHERE approved=TRUE;

View File

@ -24,8 +24,14 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ExtendWith(MockitoExtension.class)
@ -65,7 +71,7 @@ public class MappersTest {
assertValidId(p.getId());
assertTrue(p.getOriginalId().size() == 2);
assertTrue(p.getOriginalId().size() == 1);
assertEquals("10.3897/oneeco.2.e13718", p.getOriginalId().get(0));
assertValidId(p.getCollectedfrom().get(0).getKey());
@ -119,8 +125,26 @@ public class MappersTest {
assertNotNull(p.getBestaccessright());
assertEquals("OPEN", p.getBestaccessright().getClassid());
verifyRelations(p, r1, r2);
assertValidId(r1.getSource());
assertValidId(r1.getTarget());
assertValidId(r2.getSource());
assertValidId(r2.getTarget());
assertValidId(r1.getCollectedfrom().get(0).getKey());
assertValidId(r2.getCollectedfrom().get(0).getKey());
assertNotNull(r1.getDataInfo());
assertNotNull(r2.getDataInfo());
assertNotNull(r1.getDataInfo().getTrust());
assertNotNull(r2.getDataInfo().getTrust());
assertEquals(r1.getSource(), r2.getTarget());
assertEquals(r2.getSource(), r1.getTarget());
assertTrue(StringUtils.isNotBlank(r1.getRelClass()));
assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
assertTrue(StringUtils.isNotBlank(r1.getRelType()));
assertTrue(StringUtils.isNotBlank(r2.getRelType()));
assertTrue(r1.getValidated());
assertTrue(r2.getValidated());
assertEquals(r1.getValidationDate(), "2020-01-01");
assertEquals(r2.getValidationDate(), "2020-01-01");
// System.out.println(new ObjectMapper().writeValueAsString(p));
// System.out.println(new ObjectMapper().writeValueAsString(r1));
// System.out.println(new ObjectMapper().writeValueAsString(r2));
@ -158,7 +182,7 @@ public class MappersTest {
final Relation r2 = (Relation) list.get(2);
assertValidId(d.getId());
assertTrue(d.getOriginalId().size() == 2);
assertTrue(d.getOriginalId().size() == 1);
assertEquals("oai:zenodo.org:3234526", d.getOriginalId().get(0));
assertValidId(d.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
@ -211,19 +235,10 @@ public class MappersTest {
});
assertEquals("0001", d.getInstance().get(0).getRefereed().getClassid());
verifyRelations(d, r1, r2);
}
private void verifyRelations(OafEntity e, Relation r1, Relation r2) {
assertEquals(e.getId(), r1.getSource());
assertEquals(e.getId(), r2.getTarget());
assertValidId(r1.getSource());
assertValidId(r1.getTarget());
assertValidId(r2.getSource());
assertValidId(r2.getTarget());
assertValidId(r1.getCollectedfrom().get(0).getKey());
assertValidId(r2.getCollectedfrom().get(0).getKey());
assertNotNull(r1.getDataInfo());
assertNotNull(r2.getDataInfo());
assertNotNull(r1.getDataInfo().getTrust());
@ -234,6 +249,10 @@ public class MappersTest {
assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
assertTrue(StringUtils.isNotBlank(r1.getRelType()));
assertTrue(StringUtils.isNotBlank(r2.getRelType()));
assertTrue(r1.getValidated());
assertTrue(r2.getValidated());
assertEquals(r1.getValidationDate(), "2020-01-01");
assertEquals(r2.getValidationDate(), "2020-01-01");
}
@Test
@ -343,6 +362,37 @@ public class MappersTest {
assertValidId(p.getId());
assertValidId(p.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
assertEquals(1, p.getAuthor().size());
assertEquals("OPEN", p.getBestaccessright().getClassid());
assertTrue(StringUtils.isNotBlank(p.getPid().get(0).getValue()));
assertTrue(StringUtils.isNotBlank(p.getPid().get(0).getQualifier().getClassid()));
assertEquals("dataset", p.getResulttype().getClassname());
assertEquals(1, p.getInstance().size());
assertEquals("OPEN", p.getInstance().get(0).getAccessright().getClassid());
assertValidId(p.getInstance().get(0).getCollectedfrom().getKey());
assertValidId(p.getInstance().get(0).getHostedby().getKey());
assertEquals(
"http://creativecommons.org/licenses/by/3.0/de/legalcode", p.getInstance().get(0).getLicense().getValue());
assertEquals(1, p.getInstance().get(0).getUrl().size());
// System.out.println(p.getInstance().get(0).getUrl().get(0));
// System.out.println(p.getInstance().get(0).getHostedby().getValue());
System.out.println(p.getPid().get(0).getValue());
}
@Test
void testBologna() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf-bologna.xml"));
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
System.out.println("***************");
System.out.println(new ObjectMapper().writeValueAsString(list));
System.out.println("***************");
final Publication p = (Publication) list.get(0);
assertValidId(p.getId());
assertValidId(p.getCollectedfrom().get(0).getKey());
System.out.println(p.getTitle().get(0).getValue());
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
System.out.println(p.getTitle().get(0).getValue());
}

View File

@ -35,7 +35,7 @@ public class MigrateDbEntitiesApplicationTest {
private MigrateDbEntitiesApplication app;
@Mock
@Mock(lenient = true)
private ResultSet rs;
@Mock

View File

@ -1047,6 +1047,7 @@ dnet:pid_types @=@ dnet:pid_types @=@ urn @=@ urn
dnet:pid_types @=@ dnet:pid_types @=@ who @=@ WHO Identifier
dnet:pid_types @=@ dnet:pid_types @=@ drks @=@ DRKS Identifier
dnet:pid_types @=@ dnet:pid_types @=@ handle @=@ Handle
dnet:pid_types @=@ dnet:pid_types @=@ data.europa.eu @=@ EU Persistent URL
dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/ACM @=@ An ACM classification term that can be associated to your publications
dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/ARXIV @=@ An ARXIV classification term that can be associated to your publications
dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/DDC @=@ A Dewey Decimal classification term (DDC) that can be associated to your publications

View File

@ -0,0 +1,368 @@
<?xml version="1.0" encoding="UTF-8"?>
<oai:record xmlns:dr="http://www.driver-repository.eu/namespace/dr"
xmlns:dri="http://www.driver-repository.eu/namespace/dri"
xmlns:oaf="http://namespace.openaire.eu/oaf" xmlns:oai="http://www.openarchives.org/OAI/2.0/">
<oai:header>
<dri:objIdentifier>r3c4b2081b22::0007d64b38bb2b399120f9993f95d911</dri:objIdentifier>
<dri:recordIdentifier>60a0a5b0-b63c-473f-b8bc-207ea037eb3b</dri:recordIdentifier>
<dri:dateOfCollection>2021-01-28T17:24:33.095+01:00</dri:dateOfCollection>
<oaf:datasourceprefix>r3c4b2081b22</oaf:datasourceprefix>
<dr:dateOfTransformation>2021-02-03T16:57:03.099+01:00</dr:dateOfTransformation>
</oai:header>
<oai:metadata>
<datacite:resource
xmlns:datacite="http://datacite.org/schema/kernel-4"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
<datacite:identifier identifierType="URL">http://data.europa.eu/88u/dataset/60a0a5b0-b63c-473f-b8bc-207ea037eb3b</datacite:identifier>
<datacite:creators/>
<datacite:titles>
<datacite:title xml:lang="en">GMIS - Favourable feeding habitat of adult Atlantic bluefin tuna (ABFT) Monthly 1998-2017 (frequency of occurence, %)</datacite:title>
</datacite:titles>
<datacite:publisher>JRC</datacite:publisher>
<datacite:publicationYear>2019</datacite:publicationYear>
<datacite:dates>
<datacite:date dateType="Issued">2019-07-09</datacite:date>
</datacite:dates>
<datacite:resourceType resourceTypeGeneral="Dataset">Dataset</datacite:resourceType>
<datacite:descriptions>
<datacite:description descriptionType="Abstract" xml:lang="en">The favourable feeding habitat of the Atlantic bluefin tuna is daily identified linking their ecological traits with environmental variables from satellite remote sensing and physical ocean models. The feeding habitat is mostly related to the occurrence of productive oceanic features (such as eddies) that are detected by satellite sensors of ocean colour (chlorophyll-a fronts). The physical variables used are sea surface temperature and sea surface height anomaly. More information: https://fishreg.jrc.ec.europa.eu/fish-habitat, Peer-reviewed publication: http://www.sciencedirect.com/science/article/pii/S0079661116000070</datacite:description>
</datacite:descriptions>
<datacite:subjects>
<datacite:subject>protected area</datacite:subject>
<datacite:subject>environmental monitoring</datacite:subject>
<datacite:subject>oceanography</datacite:subject>
<datacite:subject>ocean</datacite:subject>
<datacite:subject>Environmental Monitoring Facilities</datacite:subject>
<datacite:subject>Environment</datacite:subject>
<datacite:subject>Protected Sites</datacite:subject>
<datacite:subject>Oceanographic Geographical Features</datacite:subject>
<datacite:subject>environmental data</datacite:subject>
<datacite:subject classid="eu-data-theme"
classname="EU Data Theme"
schemeid="dnet:subject_classification_typologies" schemename="dnet:subject_classification_typologies">http://publications.europa.eu/resource/authority/data-theme/TECH</datacite:subject>
<datacite:subject classid="eu-data-theme"
classname="EU Data Theme"
schemeid="dnet:subject_classification_typologies" schemename="dnet:subject_classification_typologies">http://publications.europa.eu/resource/authority/data-theme/ENVI</datacite:subject>
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<datacite:subject classid="eurovoc" classname="EuroVoc"
schemeid="dnet:subject_classification_typologies" schemename="dnet:subject_classification_typologies">http://eurovoc.europa.eu/2107</datacite:subject>
<datacite:subject classid="eurovoc" classname="EuroVoc"
schemeid="dnet:subject_classification_typologies" schemename="dnet:subject_classification_typologies">http://eurovoc.europa.eu/4801</datacite:subject>
<datacite:subject classid="eurovoc" classname="EuroVoc"
schemeid="dnet:subject_classification_typologies" schemename="dnet:subject_classification_typologies">http://eurovoc.europa.eu/3140</datacite:subject>
</datacite:subjects>
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<datacite:format>http://publications.europa.eu/resource/authority/file-type/OP_DATPRO</datacite:format>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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</datacite:geoLocation>
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<oaf:identifier identifierType="data.europa.eu">http://data.europa.eu/88u/dataset/60a0a5b0-b63c-473f-b8bc-207ea037eb3b</oaf:identifier>
<oaf:country>EU</oaf:country>
<oaf:accessrights>OPEN</oaf:accessrights>
<dr:CobjCategory type="dataset">0021</dr:CobjCategory>
<oaf:dateAccepted>2019-07-09</oaf:dateAccepted>
<oaf:hostedBy id="re3data_____::r3d100011728" name="European Union Open Data Portal"/>
<oaf:collectedFrom id="re3data_____::r3d100011728" name="European Union Open Data Portal"/>
<oaf:license>CC_BY_4_0</oaf:license>
<oaf:language>ENG</oaf:language>
</oai:metadata>
<about xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<provenance xmlns="http://www.openarchives.org/OAI/2.0/provenance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/provenance http://www.openarchives.org/OAI/2.0/provenance.xsd">
<originDescription altered="true" harvestDate="2021-01-28T17:24:33.095+01:00">
<baseURL>https%3A%2F%2Fdata.europa.eu%2Feuodp%2Fdata%2Fapiodp%2Faction%2Fpackage_search</baseURL>
<identifier/>
<datestamp/>
<metadataNamespace/>
</originDescription>
</provenance>
<oaf:datainfo>
<oaf:inferred>false</oaf:inferred>
<oaf:deletedbyinference>false</oaf:deletedbyinference>
<oaf:trust>0.9</oaf:trust>
<oaf:inferenceprovenance/>
<oaf:provenanceaction classid="sysimport:crosswalk"
classname="sysimport:crosswalk"
schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
</oaf:datainfo>
</about>
</oai:record>

View File

@ -46,6 +46,7 @@
<oaf:collectedFrom id="openaire____::crossref" name="Crossref"/>
<oaf:identifier identifierType="doi">10.1080/23744235.2020.1774644</oaf:identifier>
<oaf:journal eissn="2374-4243" ep="3" iss="" issn="2374-4235" sp="1" vol="">Infectious Diseases</oaf:journal>
<oaf:projectid validationDate="2020-12-07T11:15:59.627Z">corda__h2020::814530</oaf:projectid>
</metadata>
<about xmlns:oai="http://www.openarchives.org/OAI/2.0/">
<provenance xmlns="http://www.openarchives.org/OAI/2.0/provenance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/provenance http://www.openarchives.org/OAI/2.0/provenance.xsd">

View File

@ -0,0 +1,117 @@
<?xml version="1.0" encoding="UTF-8"?>
<record xmlns:datacite="http://datacite.org/schema/kernel-3"
xmlns:dr="http://www.driver-repository.eu/namespace/dr"
xmlns:oaf="http://namespace.openaire.eu/oaf" xmlns:oai="http://www.openarchives.org/OAI/2.0/">
<oai:header xmlns="http://namespace.openaire.eu/"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dri="http://www.driver-repository.eu/namespace/dri"
xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<dri:objIdentifier>r3f52792889d::00002412cb25f2f3047712d00ab2c8eb</dri:objIdentifier>
<dri:recordIdentifier>hdl:11858/00-1734-0000-0003-EE73-2</dri:recordIdentifier>
<dri:dateOfCollection>2020-12-16T10:04:03.148Z</dri:dateOfCollection>
<oaf:datasourceprefix>r3f52792889d</oaf:datasourceprefix>
<identifier xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:rn8z.0</identifier>
<datestamp xmlns="http://www.openarchives.org/OAI/2.0/">2012-01-29T20:54:12Z</datestamp>
<dr:dateOfTransformation>2020-12-16T16:02:37.562Z</dr:dateOfTransformation>
</oai:header>
<metadata>
<datacite:resource xmlns="http://www.openarchives.org/OAI/2.0/"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dri="http://www.driver-repository.eu/namespace/dri"
xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<datacite:identifier identifierType="Handle">hdl:11858/00-1734-0000-0003-EE73-2</datacite:identifier>
<datacite:creators>
<datacite:creator>
<datacite:creatorName></datacite:creatorName>
<datacite:nameIdentifier nameIdentifierScheme="pnd" schemeURI="https://ref.de.dariah.eu/pndsearch/pndquery.xql?id="></datacite:nameIdentifier>
</datacite:creator>
</datacite:creators>
<datacite:titles>
<datacite:title titleType="Other">Auf dem Trocknen</datacite:title>
<datacite:title titleType="Other">Detlev von Liliencron: Gute Nacht. Hinterlassene Gedichte, Berlin: Schuster &amp; Loeffler, 1909.</datacite:title>
</datacite:titles>
<datacite:publisher>TextGrid</datacite:publisher>
<datacite:publicationYear>2012</datacite:publicationYear>
<datacite:contributors>
<datacite:contributor contributorType="DataManager">
<datacite:contributorName>tvitt@textgrid.de</datacite:contributorName>
</datacite:contributor>
<datacite:contributor contributorType="Other">
<datacite:contributorName>Digitale Bibliothek</datacite:contributorName>
<datacite:nameIdentifier nameIdentifierScheme="textgrid" schemeURI="http://www.textgridlab.org/schema/textgrid-metadata_2010.xsd">TGPR-372fe6dc-57f2-6cd4-01b5-2c4bbefcfd3c</datacite:nameIdentifier>
</datacite:contributor>
</datacite:contributors>
<datacite:dates>
<datacite:date dateType="Created">2012-01-29T20:54:12Z</datacite:date>
<datacite:date dateType="Issued">2012-01-29T20:54:12Z</datacite:date>
<datacite:date dateType="Updated">2012-01-29T20:54:12Z</datacite:date>
</datacite:dates>
<datacite:resourceType resourceTypeGeneral="Dataset"/>
<alternateIdentifiers xmlns="http://datacite.org/schema/kernel-3">
<datacite:alternateIdentifier alternateIdentifierType="URI" xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:rn8z.0</datacite:alternateIdentifier>
<alternateIdentifier alternateIdentifierType="URL">http://hdl.handle.net/hdl:11858/00-1734-0000-0003-EE73-2</alternateIdentifier>
</alternateIdentifiers>
<datacite:relatedIdentifiers>
<datacite:relatedIdentifier relatedIdentifierType="Handle" relationType="IsPartOf">hdl:11858/00-1734-0000-0003-EE72-4</datacite:relatedIdentifier>
</datacite:relatedIdentifiers>
<datacite:sizes>
<datacite:size>527 Bytes</datacite:size>
</datacite:sizes>
<datacite:formats>
<datacite:format>text/tg.edition+tg.aggregation+xml</datacite:format>
</datacite:formats>
<datacite:version>0</datacite:version>
<datacite:rightsList>
<datacite:rights rightsURI="http://creativecommons.org/licenses/by/3.0/de/legalcode"> Der annotierte Datenbestand der Digitalen Bibliothek inklusive
Metadaten sowie davon einzeln zugängliche Teile sind eine Abwandlung
des Datenbestandes von www.editura.de durch TextGrid und werden
unter der Lizenz Creative Commons Namensnennung 3.0 Deutschland
Lizenz (by-Nennung TextGrid) veröffentlicht. Die Lizenz bezieht sich
nicht auf die der Annotation zu Grunde liegenden allgemeinfreien
Texte (Siehe auch Punkt 2 der Lizenzbestimmungen).</datacite:rights>
<datacite:rights rightsURI="info:eu-repo/semantics/openAccess"/>
</datacite:rightsList>
<datacite:descriptions>
<datacite:description descriptionType="Abstract"/>
</datacite:descriptions>
<datacite:geoLocations>
<datacite:geoLocation>
<datacite:geoLocationPlace
xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">Berlin</datacite:geoLocationPlace>
</datacite:geoLocation>
</datacite:geoLocations>
</datacite:resource>
<oaf:identifier identifierType="handle">hdl:11858/00-1734-0000-0003-EE73-2</oaf:identifier>
<dr:CobjCategory type="dataset">0021</dr:CobjCategory>
<oaf:refereed>0002</oaf:refereed>
<oaf:dateAccepted>2012-01-29</oaf:dateAccepted>
<oaf:accessrights>OPEN</oaf:accessrights>
<oaf:license>http://creativecommons.org/licenses/by/3.0/de/legalcode</oaf:license>
<oaf:language>und</oaf:language>
<oaf:country>DE</oaf:country>
<oaf:hostedBy id="re3data_____::r3d100011365" name="TextGrid Repository"/>
<oaf:collectedFrom id="re3data_____::r3d100011365" name="TextGrid Repository"/>
</metadata>
<about xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dri="http://www.driver-repository.eu/namespace/dri"
xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<provenance xmlns="http://www.openarchives.org/OAI/2.0/provenance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/provenance http://www.openarchives.org/OAI/2.0/provenance.xsd">
<originDescription altered="true" harvestDate="2020-12-16T10:04:03.148Z">
<baseURL>https%3A%2F%2Fdev.textgridlab.org%2F1.0%2Ftgoaipmh%2Foai</baseURL>
<identifier>textgrid:rn8z.0</identifier>
<datestamp>2012-01-29T20:54:12Z</datestamp>
<metadataNamespace/>
</originDescription>
</provenance>
<oaf:datainfo>
<oaf:inferred>false</oaf:inferred>
<oaf:deletedbyinference>false</oaf:deletedbyinference>
<oaf:trust>0.9</oaf:trust>
<oaf:inferenceprovenance/>
<oaf:provenanceaction classid="sysimport:crosswalk:datasetarchive"
classname="sysimport:crosswalk:datasetarchive"
schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
</oaf:datainfo>
</about>
</record>

View File

@ -6,29 +6,29 @@
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dri="http://www.driver-repository.eu/namespace/dri"
xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<dri:objIdentifier>r3f52792889d::000051aa1f61d77d2c0b340091f8024e</dri:objIdentifier>
<dri:recordIdentifier>textgrid:q9cv.0</dri:recordIdentifier>
<dri:dateOfCollection>2020-11-17T09:34:11.128+01:00</dri:dateOfCollection>
<dri:objIdentifier>r3f52792889d::00002412cb25f2f3047712d00ab2c8eb</dri:objIdentifier>
<dri:recordIdentifier>hdl:11858/00-1734-0000-0003-EE73-2</dri:recordIdentifier>
<dri:dateOfCollection>2020-12-16T10:04:03.148Z</dri:dateOfCollection>
<oaf:datasourceprefix>r3f52792889d</oaf:datasourceprefix>
<identifier xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:q9cv.0</identifier>
<datestamp xmlns="http://www.openarchives.org/OAI/2.0/">2012-01-21T13:35:20Z</datestamp>
<dr:dateOfTransformation>2020-11-17T19:08:56.703+01:00</dr:dateOfTransformation>
<identifier xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:rn8z.0</identifier>
<datestamp xmlns="http://www.openarchives.org/OAI/2.0/">2012-01-29T20:54:12Z</datestamp>
<dr:dateOfTransformation>2020-12-16T16:02:37.562Z</dr:dateOfTransformation>
</oai:header>
<metadata>
<datacite:resource xmlns="http://www.openarchives.org/OAI/2.0/"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dri="http://www.driver-repository.eu/namespace/dri"
xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<datacite:identifier identifierType="Handle">hdl:11858/00-1734-0000-0003-7664-F</datacite:identifier>
<datacite:identifier identifierType="Handle">hdl:11858/00-1734-0000-0003-EE73-2</datacite:identifier>
<datacite:creators>
<datacite:creator>
<datacite:creatorName>Hoffmann von Fallersleben, August Heinrich</datacite:creatorName>
<datacite:nameIdentifier nameIdentifierScheme="pnd" schemeURI="https://de.dariah.eu/pnd-service">118552589</datacite:nameIdentifier>
<datacite:creatorName>Liliencron, Detlev von</datacite:creatorName>
<datacite:nameIdentifier nameIdentifierScheme="pnd" schemeURI="https://ref.de.dariah.eu/pndsearch/pndquery.xql?id=">118572954</datacite:nameIdentifier>
</datacite:creator>
</datacite:creators>
<datacite:titles>
<datacite:title titleType="Other">Mailied</datacite:title>
<datacite:title titleType="Other">August Heinrich Hoffmann von Fallersleben: Unpolitische Lieder von Hoffmann von Fallersleben, 1. + 2. Theil, 1. Theil, Hamburg: Hoffmann und Campe, 1841.</datacite:title>
<datacite:title titleType="Other">Auf dem Trocknen</datacite:title>
<datacite:title titleType="Other">Detlev von Liliencron: Gute Nacht. Hinterlassene Gedichte, Berlin: Schuster &amp; Loeffler, 1909.</datacite:title>
</datacite:titles>
<datacite:publisher>TextGrid</datacite:publisher>
<datacite:publicationYear>2012</datacite:publicationYear>
@ -38,21 +38,21 @@
</datacite:contributor>
<datacite:contributor contributorType="Other">
<datacite:contributorName>Digitale Bibliothek</datacite:contributorName>
<datacite:nameIdentifier nameIdentifierScheme="textgrid">TGPR-372fe6dc-57f2-6cd4-01b5-2c4bbefcfd3c</datacite:nameIdentifier>
<datacite:nameIdentifier nameIdentifierScheme="textgrid" schemeURI="http://www.textgridlab.org/schema/textgrid-metadata_2010.xsd">TGPR-372fe6dc-57f2-6cd4-01b5-2c4bbefcfd3c</datacite:nameIdentifier>
</datacite:contributor>
</datacite:contributors>
<datacite:dates>
<datacite:date dateType="Created">2012-01-21T13:35:20Z</datacite:date>
<datacite:date dateType="Issued">2012-01-21T13:35:20Z</datacite:date>
<datacite:date dateType="Updated">2012-01-21T13:35:20Z</datacite:date>
<datacite:date dateType="Created">2012-01-29T20:54:12Z</datacite:date>
<datacite:date dateType="Issued">2012-01-29T20:54:12Z</datacite:date>
<datacite:date dateType="Updated">2012-01-29T20:54:12Z</datacite:date>
</datacite:dates>
<datacite:resourceType resourceTypeGeneral="Dataset"/>
<alternateIdentifiers xmlns="http://datacite.org/schema/kernel-3">
<datacite:alternateIdentifier alternateIdentifierType="URI" xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:q9cv.0</datacite:alternateIdentifier>
<alternateIdentifier alternateIdentifierType="URL">http://hdl.handle.net/hdl:11858/00-1734-0000-0003-7664-F</alternateIdentifier>
<datacite:alternateIdentifier alternateIdentifierType="URI" xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:rn8z.0</datacite:alternateIdentifier>
<alternateIdentifier alternateIdentifierType="URL">http://hdl.handle.net/hdl:11858/00-1734-0000-0003-EE73-2</alternateIdentifier>
</alternateIdentifiers>
<datacite:relatedIdentifiers>
<datacite:relatedIdentifier relatedIdentifierType="Handle" relationType="IsPartOf">hdl:11858/00-1734-0000-0003-7666-B</datacite:relatedIdentifier>
<datacite:relatedIdentifier relatedIdentifierType="Handle" relationType="IsPartOf">hdl:11858/00-1734-0000-0003-EE72-4</datacite:relatedIdentifier>
</datacite:relatedIdentifiers>
<datacite:sizes>
<datacite:size>527 Bytes</datacite:size>
@ -77,17 +77,18 @@
<datacite:geoLocations>
<datacite:geoLocation>
<datacite:geoLocationPlace
xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">Hamburg</datacite:geoLocationPlace>
xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">Berlin</datacite:geoLocationPlace>
</datacite:geoLocation>
</datacite:geoLocations>
</datacite:resource>
<oaf:identifier identifierType="handle">hdl:11858/00-1734-0000-0003-7664-F</oaf:identifier>
<oaf:identifier identifierType="handle">hdl:11858/00-1734-0000-0003-EE73-2</oaf:identifier>
<dr:CobjCategory type="dataset">0021</dr:CobjCategory>
<oaf:refereed>0002</oaf:refereed>
<oaf:dateAccepted>2012-01-21</oaf:dateAccepted>
<oaf:dateAccepted>2012-01-29</oaf:dateAccepted>
<oaf:accessrights>OPEN</oaf:accessrights>
<oaf:license>http://creativecommons.org/licenses/by/3.0/de/legalcode</oaf:license>
<oaf:language>und</oaf:language>
<oaf:country>DE</oaf:country>
<oaf:hostedBy id="re3data_____::r3d100011365" name="TextGrid Repository"/>
<oaf:collectedFrom id="re3data_____::r3d100011365" name="TextGrid Repository"/>
</metadata>
@ -95,11 +96,11 @@
xmlns:dri="http://www.driver-repository.eu/namespace/dri"
xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<provenance xmlns="http://www.openarchives.org/OAI/2.0/provenance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/provenance http://www.openarchives.org/OAI/2.0/provenance.xsd">
<originDescription altered="true" harvestDate="2020-11-17T09:34:11.128+01:00">
<originDescription altered="true" harvestDate="2020-12-16T10:04:03.148Z">
<baseURL>https%3A%2F%2Fdev.textgridlab.org%2F1.0%2Ftgoaipmh%2Foai</baseURL>
<identifier>textgrid:q9cv.0</identifier>
<datestamp>2012-01-21T13:35:20Z</datestamp>
<metadataNamespace>http://schema.datacite.org/oai/oai-1.0/</metadataNamespace>
<identifier>textgrid:rn8z.0</identifier>
<datestamp>2012-01-29T20:54:12Z</datestamp>
<metadataNamespace/>
</originDescription>
</provenance>
<oaf:datainfo>
@ -107,9 +108,10 @@
<oaf:deletedbyinference>false</oaf:deletedbyinference>
<oaf:trust>0.9</oaf:trust>
<oaf:inferenceprovenance/>
<oaf:provenanceaction classid="sysimport:crosswalk"
classname="sysimport:crosswalk"
<oaf:provenanceaction classid="sysimport:crosswalk:datasetarchive"
classname="sysimport:crosswalk:datasetarchive"
schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
</oaf:datainfo>
</about>
</record>

View File

@ -1,15 +1,15 @@
package eu.dnetlib.dhp.export
import com.fasterxml.jackson.databind.ObjectMapper
import java.time.LocalDateTime
import java.time.format.DateTimeFormatter
import eu.dnetlib.dhp.common.PacePerson
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{Author, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.schema.oaf.{Author, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import org.codehaus.jackson.map.ObjectMapper
import eu.dnetlib.dhp.schema.scholexplorer.OafUtils._
import scala.collection.JavaConverters._

View File

@ -1,27 +1,21 @@
package eu.dnetlib.dhp.`export`
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Instance, Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication}
import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.Text
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.hadoop.mapred.SequenceFileOutputFormat
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql.functions._
import org.apache.spark.sql.expressions.Window
import org.apache.spark.{SparkConf, SparkContext}
import org.codehaus.jackson.map.ObjectMapper
import org.apache.spark.SparkConf
import scala.collection.mutable.ArrayBuffer
import scala.collection.JavaConverters._
object SparkExportContentForOpenAire {
def main(args: Array[String]): Unit = {
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkExportContentForOpenAire.getClass.getResourceAsStream("input_export_content_parameters.json")))
@ -178,11 +172,4 @@ object SparkExportContentForOpenAire {
fRels.union(fpubs).union(fdats).rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingPath/export/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
}
}

View File

@ -10,7 +10,8 @@ import org.apache.http.client.methods.HttpPut;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.codehaus.jackson.map.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;

View File

@ -1,5 +1,6 @@
package eu.dnetlib.dhp.provision
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.provision.scholix.Scholix
import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary
@ -7,7 +8,6 @@ import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.codehaus.jackson.map.ObjectMapper
object SparkConvertDatasetToJson {

View File

@ -54,6 +54,13 @@
<artifactId>spark-solr</artifactId>
</dependency>
<!-- the solr-test-framework requires the old junit:junit test framework -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.solr</groupId>
<artifactId>solr-test-framework</artifactId>
@ -140,6 +147,12 @@
<dependency>
<groupId>org.apache.zookeeper</groupId>
<artifactId>zookeeper</artifactId>
<exclusions>
<exclusion>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</exclusion>
</exclusions>
</dependency>

View File

@ -27,6 +27,7 @@ import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2;
@ -272,11 +273,7 @@ public class CreateRelatedEntitiesJob_phase2 {
.filter(Objects::nonNull)
.map(Qualifier::getClassid)
.filter(StringUtils::isNotBlank)
.anyMatch(c -> "orcid".equals(c.toLowerCase()));
}
private static FilterFunction<JoinedEntity> filterEmptyEntityFn() {
return (FilterFunction<JoinedEntity>) v -> Objects.nonNull(v.getEntity());
.anyMatch(c -> c.toLowerCase().contains(ModelConstants.ORCID));
}
private static void removeOutputDir(SparkSession spark, String path) {

View File

@ -0,0 +1,52 @@
package eu.dnetlib.dhp.oa.provision.utils;
import java.util.Comparator;
import java.util.Optional;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class AuthorPidTypeComparator implements Comparator<StructuredProperty> {
@Override
public int compare(StructuredProperty left, StructuredProperty right) {
String lClass = Optional
.ofNullable(left)
.map(StructuredProperty::getQualifier)
.map(Qualifier::getClassid)
.orElse(null);
String rClass = Optional
.ofNullable(right)
.map(StructuredProperty::getQualifier)
.map(Qualifier::getClassid)
.orElse(null);
if (lClass == null && rClass == null)
return 0;
if (lClass == null)
return 1;
if (rClass == null)
return -1;
if (lClass.equals(rClass))
return 0;
if (lClass.equals(ModelConstants.ORCID))
return -1;
if (rClass.equals(ModelConstants.ORCID))
return 1;
if (lClass.equals(ModelConstants.ORCID_PENDING))
return -1;
if (rClass.equals(ModelConstants.ORCID_PENDING))
return 1;
return 0;
}
}

View File

@ -7,13 +7,16 @@ import java.util.Set;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
public class GraphMappingUtils {
public static final String SEPARATOR = "_";
public static Set<String> authorPidTypes = Sets.newHashSet("orcid", "magidentifier");
public static Set<String> authorPidTypes = Sets
.newHashSet(
ModelConstants.ORCID, ModelConstants.ORCID_PENDING, "magidentifier");
public static String removePrefix(final String s) {
if (s.contains("|"))

View File

@ -73,7 +73,9 @@ public class TemplateFactory {
final Collection<String> fields,
final String semanticclass,
final String semantischeme,
final DataInfo info) {
final DataInfo info,
final boolean validated,
final String validationDate) {
return getTemplate(resources.getRel())
.add("type", type)
.add("objIdentifier", escapeXml(removePrefix(objIdentifier)))
@ -86,6 +88,8 @@ public class TemplateFactory {
.add(
"provenanceaction",
info.getProvenanceaction() != null ? info.getProvenanceaction().getClassid() : "")
.add("validated", validated)
.add("validationdate", validationDate)
.render();
}

View File

@ -254,6 +254,18 @@ public class XmlRecordFactory implements Serializable {
p -> p,
(p1, p2) -> p1))
.values()
.stream()
.collect(
Collectors
.groupingBy(
p -> p.getValue(),
Collectors
.mapping(
p -> p,
Collectors.minBy(new AuthorPidTypeComparator()))))
.values()
.stream()
.map(op -> op.get())
.forEach(
sp -> {
String pidType = getAuthorPidType(sp.getQualifier().getClassid());
@ -1082,9 +1094,12 @@ public class XmlRecordFactory implements Serializable {
String.format("missing scheme for: <%s - %s>", type.toString(), targetType));
}
final HashSet<String> fields = Sets.newHashSet(mapFields(link, contexts));
if (rel.getValidated() == null)
rel.setValidated(false);
return templateFactory
.getRel(
targetType, rel.getTarget(), fields, rel.getRelClass(), scheme, rel.getDataInfo());
targetType, rel.getTarget(), fields, rel.getRelClass(), scheme, rel.getDataInfo(), rel.getValidated(),
rel.getValidationDate());
}
private List<String> listChildren(

View File

@ -1,4 +1,5 @@
<rel inferred="$inferred$" trust="$trust$" inferenceprovenance="$inferenceprovenance$" provenanceaction="$provenanceaction$">
<to class="$class$" scheme="$scheme$" type="$type$">$objIdentifier$</to>
$if(validated)$<validated date="$validationdate$"/>$else$$endif$
<to class="$class$" scheme="$scheme$" type="$type$">$objIdentifier$</to>
$metadata:{ it | $it$ }$
</rel>

View File

@ -6,15 +6,13 @@ import org.apache.solr.client.solrj.response.UpdateResponse;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import junit.framework.Assert;
public class SolrAdminApplicationTest extends SolrTest {
@Test
public void testPing() throws Exception {
SolrPingResponse pingResponse = miniCluster.getSolrClient().ping();
log.info("pingResponse: '{}'", pingResponse.getStatus());
Assert.assertTrue(pingResponse.getStatus() == 0);
Assertions.assertTrue(pingResponse.getStatus() == 0);
}
@Test

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