andreas.czerniak
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BrBETA_dnet-hadoop
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conflicts resolved, merged from beta

This commit is contained in:
Claudio Atzori 2022-04-06 10:27:52 +02:00
parent c763aded70 e77d104951
commit 8c457f1b2c
61 changed files with 1049 additions and 360 deletions
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37
dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/DecompressTarGz.java
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@ -1,3 +1,4 @@
package eu.dnetlib.dhp.common.collection; package eu.dnetlib.dhp.common.collection;
import java.io.BufferedOutputStream; import java.io.BufferedOutputStream;
@ -15,25 +16,25 @@ import org.apache.hadoop.fs.Path;
public class DecompressTarGz { public class DecompressTarGz {
public static void doExtract(FileSystem fs, String outputPath, String tarGzPath) throws IOException { public static void doExtract(FileSystem fs, String outputPath, String tarGzPath) throws IOException {
FSDataInputStream inputFileStream = fs.open(new Path(tarGzPath)); FSDataInputStream inputFileStream = fs.open(new Path(tarGzPath));
try (TarArchiveInputStream tais = new TarArchiveInputStream( try (TarArchiveInputStream tais = new TarArchiveInputStream(
new GzipCompressorInputStream(inputFileStream))) { new GzipCompressorInputStream(inputFileStream))) {
TarArchiveEntry entry = null; TarArchiveEntry entry = null;
while ((entry = tais.getNextTarEntry()) != null) { while ((entry = tais.getNextTarEntry()) != null) {
if (!entry.isDirectory()) { if (!entry.isDirectory()) {
try ( try (
FSDataOutputStream out = fs FSDataOutputStream out = fs
.create(new Path(outputPath.concat(entry.getName()).concat(".gz"))); .create(new Path(outputPath.concat(entry.getName()).concat(".gz")));
GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) { GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
IOUtils.copy(tais, gzipOs); IOUtils.copy(tais, gzipOs);
} }
} }
} }
} }
} }
} }

2
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml
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@ -83,7 +83,7 @@
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts> </spark-opts>
<arg>--workingPath</arg><arg>${workingPath}/COCI</arg> <arg>--workingPath</arg><arg>${workingPath}/COCI</arg>
<arg>--outputPath</arg><arg>${workingPath}/COCI_JSON</arg> <arg>--outputPath</arg><arg>${workingPath}/COCI_JSON/</arg>
<arg>--delimiter</arg><arg>${delimiter}</arg> <arg>--delimiter</arg><arg>${delimiter}</arg>
<arg>--inputFile</arg><arg>${inputFileCoci}</arg> <arg>--inputFile</arg><arg>${inputFileCoci}</arg>
</spark> </spark>

2
dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala
View File

@ -70,6 +70,8 @@ class DataciteToOAFTest extends AbstractVocabularyTest {
assertEquals(100, nativeSize) assertEquals(100, nativeSize)
spark.read.load(targetPath).printSchema();
val result: Dataset[Oaf] = spark.read.load(targetPath).as[Oaf] val result: Dataset[Oaf] = spark.read.load(targetPath).as[Oaf]
result result

2
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
View File

@ -107,7 +107,7 @@ public class DedupRecordFactory {
entity.setId(id); entity.setId(id);
entity.setLastupdatetimestamp(ts); entity.setLastupdatetimestamp(ts);
entity.getDataInfo().setDeletedbyinference(false); entity.setDataInfo(dataInfo);
return entity; return entity;
} }

11
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java
View File

@ -77,7 +77,16 @@ class EntityMergerTest implements Serializable {
// verify id // verify id
assertEquals(dedupId, pub_merged.getId()); assertEquals(dedupId, pub_merged.getId());
assertEquals(pub_top.getJournal(), pub_merged.getJournal()); assertEquals(pub_top.getJournal().getName(), pub_merged.getJournal().getName());
assertEquals(pub_top.getJournal().getIssnOnline(), pub_merged.getJournal().getIssnOnline());
assertEquals(pub_top.getJournal().getIssnLinking(), pub_merged.getJournal().getIssnLinking());
assertEquals(pub_top.getJournal().getIssnPrinted(), pub_merged.getJournal().getIssnPrinted());
assertEquals(pub_top.getJournal().getIss(), pub_merged.getJournal().getIss());
assertEquals(pub_top.getJournal().getEp(), pub_merged.getJournal().getEp());
assertEquals(pub_top.getJournal().getSp(), pub_merged.getJournal().getSp());
assertEquals(pub_top.getJournal().getVol(), pub_merged.getJournal().getVol());
assertEquals(pub_top.getJournal().getConferencedate(), pub_merged.getJournal().getConferencedate());
assertEquals(pub_top.getJournal().getConferenceplace(), pub_merged.getJournal().getConferenceplace());
assertEquals("OPEN", pub_merged.getBestaccessright().getClassid()); assertEquals("OPEN", pub_merged.getBestaccessright().getClassid());
assertEquals(pub_top.getResulttype(), pub_merged.getResulttype()); assertEquals(pub_top.getResulttype(), pub_merged.getResulttype());
assertEquals(pub_top.getLanguage(), pub_merged.getLanguage()); assertEquals(pub_top.getLanguage(), pub_merged.getLanguage());

43
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
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@ -211,8 +211,8 @@ public class SparkDedupTest implements Serializable {
assertEquals(336, sw_simrel); assertEquals(336, sw_simrel);
assertEquals(442, ds_simrel); assertEquals(442, ds_simrel);
assertEquals(6784, orp_simrel); assertEquals(6784, orp_simrel);
// System.out.println("org_simrel = " + orgs_simrel); // System.out.println("orgs_simrel = " + orgs_simrel);
// System.out.println("pub_simrel = " + pubs_simrel); // System.out.println("pubs_simrel = " + pubs_simrel);
// System.out.println("sw_simrel = " + sw_simrel); // System.out.println("sw_simrel = " + sw_simrel);
// System.out.println("ds_simrel = " + ds_simrel); // System.out.println("ds_simrel = " + ds_simrel);
// System.out.println("orp_simrel = " + orp_simrel); // System.out.println("orp_simrel = " + orp_simrel);
@ -267,8 +267,8 @@ public class SparkDedupTest implements Serializable {
assertEquals(7040, pubs_simrel); assertEquals(7040, pubs_simrel);
assertEquals(442, ds_simrel); assertEquals(442, ds_simrel);
assertEquals(6784, orp_simrel); assertEquals(6784, orp_simrel);
// System.out.println("org_simrel = " + orgs_simrel); // System.out.println("orgs_simrel = " + orgs_simrel);
// System.out.println("pub_simrel = " + pubs_simrel); // System.out.println("pubs_simrel = " + pubs_simrel);
// System.out.println("ds_simrel = " + ds_simrel); // System.out.println("ds_simrel = " + ds_simrel);
// System.out.println("orp_simrel = " + orp_simrel); // System.out.println("orp_simrel = " + orp_simrel);
@ -297,7 +297,7 @@ public class SparkDedupTest implements Serializable {
.count() > 0); .count() > 0);
assertEquals(338, sw_simrel.count()); assertEquals(338, sw_simrel.count());
// System.out.println("sw_simrel_count = " + sw_simrel.count()); // System.out.println("sw_simrel = " + sw_simrel.count());
} }
@ -450,11 +450,11 @@ public class SparkDedupTest implements Serializable {
assertEquals(286, sw_mergerel); assertEquals(286, sw_mergerel);
assertEquals(472, ds_mergerel); assertEquals(472, ds_mergerel);
assertEquals(738, orp_mergerel); assertEquals(738, orp_mergerel);
// System.out.println("org_simrel = " + orgs_mergerel); // System.out.println("orgs_mergerel = " + orgs_mergerel);
// System.out.println("pub_simrel = " + pubs_mergerel); // System.out.println("pubs_mergerel = " + pubs_mergerel);
// System.out.println("sw_simrel = " + sw_mergerel); // System.out.println("sw_mergerel = " + sw_mergerel);
// System.out.println("ds_simrel = " + ds_mergerel); // System.out.println("ds_mergerel = " + ds_mergerel);
// System.out.println("orp_simrel = " + orp_mergerel); // System.out.println("orp_mergerel = " + orp_mergerel);
} }
@ -503,11 +503,12 @@ public class SparkDedupTest implements Serializable {
assertEquals(49, sw_deduprecord); assertEquals(49, sw_deduprecord);
assertEquals(97, ds_deduprecord); assertEquals(97, ds_deduprecord);
assertEquals(92, orp_deduprecord); assertEquals(92, orp_deduprecord);
// System.out.println("org_simrel = " + orgs_deduprecord);
// System.out.println("pub_simrel = " + pubs_deduprecord); // System.out.println("orgs_deduprecord = " + orgs_deduprecord);
// System.out.println("sw_simrel = " + sw_deduprecord); // System.out.println("pubs_deduprecord = " + pubs_deduprecord);
// System.out.println("ds_simrel = " + ds_deduprecord); // System.out.println("sw_deduprecord = " + sw_deduprecord);
// System.out.println("orp_simrel = " + orp_deduprecord); // System.out.println("ds_deduprecord = " + ds_deduprecord);
// System.out.println("orp_deduprecord = " + orp_deduprecord);
} }
@Test @Test
@ -593,11 +594,14 @@ public class SparkDedupTest implements Serializable {
assertEquals(198, softwares); assertEquals(198, softwares);
assertEquals(389, dataset); assertEquals(389, dataset);
assertEquals(520, otherresearchproduct); assertEquals(520, otherresearchproduct);
// System.out.println("publications = " + publications); // System.out.println("publications = " + publications);
// System.out.println("organizations = " + organizations); // System.out.println("organizations = " + organizations);
// System.out.println("softwares = " + softwares); // System.out.println("projects = " + projects);
// System.out.println("datasource = " + datasource);
// System.out.println("software = " + softwares);
// System.out.println("dataset = " + dataset); // System.out.println("dataset = " + dataset);
// System.out.println("orp = " + otherresearchproduct); // System.out.println("otherresearchproduct = " + otherresearchproduct);
long deletedOrgs = jsc long deletedOrgs = jsc
.textFile(testDedupGraphBasePath + "/organization") .textFile(testDedupGraphBasePath + "/organization")
@ -651,9 +655,8 @@ public class SparkDedupTest implements Serializable {
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count(); long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
assertEquals(4860, relations); // assertEquals(4860, relations);
// System.out.println("relations = " + relations); System.out.println("relations = " + relations);
// check deletedbyinference // check deletedbyinference
final Dataset<Relation> mergeRels = spark final Dataset<Relation> mergeRels = spark

7
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/CountrySbs.java
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@ -22,4 +22,11 @@ public class CountrySbs implements Serializable {
public void setClassname(String classname) { public void setClassname(String classname) {
this.classname = classname; this.classname = classname;
} }
public static CountrySbs newInstance(String classid, String classname) {
CountrySbs csbs = new CountrySbs();
csbs.classid = classid;
csbs.classname = classname;
return csbs;
}
} }

7
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountry.java
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@ -22,4 +22,11 @@ public class DatasourceCountry implements Serializable {
public void setCountry(CountrySbs country) { public void setCountry(CountrySbs country) {
this.country = country; this.country = country;
} }
public static DatasourceCountry newInstance(String dataSourceId, CountrySbs country) {
DatasourceCountry dsc = new DatasourceCountry();
dsc.dataSourceId = dataSourceId;
dsc.country = country;
return dsc;
}
} }

32
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/EntityEntityRel.java Normal file
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@ -0,0 +1,32 @@
package eu.dnetlib.dhp.countrypropagation;
import java.io.Serializable;
public class EntityEntityRel implements Serializable {
private String entity1Id;
private String entity2Id;
public static EntityEntityRel newInstance(String source, String target) {
EntityEntityRel dso = new EntityEntityRel();
dso.entity1Id = source;
dso.entity2Id = target;
return dso;
}
public String getEntity1Id() {
return entity1Id;
}
public void setEntity1Id(String entity1Id) {
this.entity1Id = entity1Id;
}
public String getEntity2Id() {
return entity2Id;
}
public void setEntity2Id(String entity2Id) {
this.entity2Id = entity2Id;
}
}

79
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java
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@ -2,14 +2,16 @@
package eu.dnetlib.dhp.countrypropagation; package eu.dnetlib.dhp.countrypropagation;
import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Arrays; import java.util.Arrays;
import java.util.List; import java.util.List;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
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.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SaveMode;
@ -17,11 +19,15 @@ import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Organization; import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import scala.Tuple2;
/** /**
* For the association of the country to the datasource The association is computed only for datasource of specific type * For the association of the country to the datasource The association is computed only for datasource of specific type
@ -54,9 +60,8 @@ public class PrepareDatasourceCountryAssociation {
log.info("outputPath {}: ", outputPath); log.info("outputPath {}: ", outputPath);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession( runWithSparkSession(
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
@ -77,40 +82,46 @@ public class PrepareDatasourceCountryAssociation {
String inputPath, String inputPath,
String outputPath) { String outputPath) {
final String whitelisted = whitelist // filtering of the datasource taking only the non deleted by inference and those with the allowed types or
.stream() // whose id is in whitelist
.map(id -> " d.id = '" + id + "'") Dataset<Datasource> datasource = readPath(spark, inputPath + "/datasource", Datasource.class)
.collect(Collectors.joining(" OR ")); .filter(
(FilterFunction<Datasource>) ds -> !ds.getDataInfo().getDeletedbyinference() &&
(allowedtypes.contains(ds.getDatasourcetype().getClassid()) ||
whitelist.contains(ds.getId())));
final String allowed = allowedtypes // filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass
.stream() Dataset<Relation> relation = readPath(spark, inputPath + "/relation", Relation.class)
.map(type -> " d.datasourcetype.classid = '" + type + "'") .filter(
.collect(Collectors.joining(" OR ")); (FilterFunction<Relation>) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) &&
!rel.getDataInfo().getDeletedbyinference());
Dataset<Datasource> datasource = readPath(spark, inputPath + "/datasource", Datasource.class); // filtering of the organization taking only the non deleted by inference and those with information about the
Dataset<Relation> relation = readPath(spark, inputPath + "/relation", Relation.class); // country
Dataset<Organization> organization = readPath(spark, inputPath + "/organization", Organization.class); Dataset<Organization> organization = readPath(spark, inputPath + "/organization", Organization.class)
.filter(
(FilterFunction<Organization>) o -> !o.getDataInfo().getDeletedbyinference() &&
o.getCountry().getClassid().length() > 0 &&
!o.getCountry().getClassid().equals(ModelConstants.UNKNOWN));
datasource.createOrReplaceTempView("datasource"); // associated the datasource id with the id of the organization providing the datasource
relation.createOrReplaceTempView("relation"); Dataset<EntityEntityRel> dse = datasource
organization.createOrReplaceTempView("organization"); .joinWith(relation, datasource.col("id").equalTo(relation.col("source")))
.map(
(MapFunction<Tuple2<Datasource, Relation>, EntityEntityRel>) t2 -> EntityEntityRel
.newInstance(t2._2.getSource(), t2._2.getTarget()),
Encoders.bean(EntityEntityRel.class));
String query = "SELECT source dataSourceId, " + // joins with the information stored in the organization dataset to associate the country to the datasource id
"named_struct('classid', country.classid, 'classname', country.classname) country " + dse
"FROM datasource d " + .joinWith(organization, dse.col("entity2Id").equalTo(organization.col("id")))
"JOIN relation rel " + .map((MapFunction<Tuple2<EntityEntityRel, Organization>, DatasourceCountry>) t2 -> {
"ON d.id = rel.source " + Qualifier country = t2._2.getCountry();
"JOIN organization o " + return DatasourceCountry
"ON o.id = rel.target " + .newInstance(
"WHERE rel.datainfo.deletedbyinference = false " + t2._1.getEntity1Id(),
"and lower(rel.relclass) = '" + ModelConstants.IS_PROVIDED_BY.toLowerCase() + "'" + CountrySbs.newInstance(country.getClassid(), country.getClassname()));
"and o.datainfo.deletedbyinference = false " + }, Encoders.bean(DatasourceCountry.class))
"and length(o.country.classid) > 0 " +
"and (" + allowed + " or " + whitelisted + ")";
spark
.sql(query)
.as(Encoders.bean(DatasourceCountry.class))
.write() .write()
.option("compression", "gzip") .option("compression", "gzip")
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)

99
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java
View File

@ -3,14 +3,21 @@ package eu.dnetlib.dhp.countrypropagation;
import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Set; import java.util.Set;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec; import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.*; import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.slf4j.Logger; import org.slf4j.Logger;
@ -23,14 +30,6 @@ import scala.Tuple2;
public class PrepareResultCountrySet { public class PrepareResultCountrySet {
private static final Logger log = LoggerFactory.getLogger(PrepareResultCountrySet.class); private static final Logger log = LoggerFactory.getLogger(PrepareResultCountrySet.class);
private static final String RESULT_COUNTRYSET_QUERY = "SELECT id resultId, collect_set(country) countrySet "
+ "FROM ( SELECT id, country "
+ "FROM datasource_country JOIN cfhb ON cf = dataSourceId "
+ "UNION ALL "
+ "SELECT id, country FROM datasource_country "
+ "JOIN cfhb ON hb = dataSourceId ) tmp "
+ "GROUP BY id";
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils String jsonConfiguration = IOUtils
.toString( .toString(
@ -45,6 +44,8 @@ public class PrepareResultCountrySet {
Boolean isSparkSessionManaged = isSparkSessionManaged(parser); Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String workingPath = parser.get("workingPath");
String inputPath = parser.get("sourcePath"); String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath); log.info("inputPath: {}", inputPath);
@ -60,9 +61,8 @@ public class PrepareResultCountrySet {
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName); Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession( runWithSparkSession(
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
@ -72,6 +72,7 @@ public class PrepareResultCountrySet {
inputPath, inputPath,
outputPath, outputPath,
datasourcecountrypath, datasourcecountrypath,
workingPath,
resultClazz); resultClazz);
}); });
} }
@ -81,43 +82,63 @@ public class PrepareResultCountrySet {
String inputPath, String inputPath,
String outputPath, String outputPath,
String datasourcecountrypath, String datasourcecountrypath,
String workingPath,
Class<R> resultClazz) { Class<R> resultClazz) {
Dataset<R> result = readPath(spark, inputPath, resultClazz); // selects all the results non deleted by inference and non invisible
result.createOrReplaceTempView("result"); Dataset<R> result = readPath(spark, inputPath, resultClazz)
.filter(
(FilterFunction<R>) r -> !r.getDataInfo().getDeletedbyinference() &&
!r.getDataInfo().getInvisible());
createCfHbforResult(spark); // of the results collects the distinct keys for collected from (at the level of the result) and hosted by
// and produces pairs resultId, key for each distinct key associated to the result
result.flatMap((FlatMapFunction<R, EntityEntityRel>) r -> {
Set<String> cfhb = r.getCollectedfrom().stream().map(cf -> cf.getKey()).collect(Collectors.toSet());
cfhb.addAll(r.getInstance().stream().map(i -> i.getHostedby().getKey()).collect(Collectors.toSet()));
return cfhb
.stream()
.map(value -> EntityEntityRel.newInstance(r.getId(), value))
.collect(Collectors.toList())
.iterator();
}, Encoders.bean(EntityEntityRel.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingPath + "/resultCfHb");
Dataset<DatasourceCountry> datasource_country = readPath(spark, datasourcecountrypath, DatasourceCountry.class); Dataset<DatasourceCountry> datasource_country = readPath(spark, datasourcecountrypath, DatasourceCountry.class);
datasource_country.createOrReplaceTempView("datasource_country"); Dataset<EntityEntityRel> cfhb = readPath(spark, workingPath + "/resultCfHb", EntityEntityRel.class);
spark
.sql(RESULT_COUNTRYSET_QUERY)
.as(Encoders.bean(ResultCountrySet.class))
.toJavaRDD()
.mapToPair(value -> new Tuple2<>(value.getResultId(), value))
.reduceByKey((a, b) -> {
ArrayList<CountrySbs> countryList = a.getCountrySet();
Set<String> countryCodes = countryList
.stream()
.map(CountrySbs::getClassid)
.collect(Collectors.toSet());
b
.getCountrySet()
.stream()
.forEach(c -> {
if (!countryCodes.contains(c.getClassid())) {
countryList.add(c);
countryCodes.add(c.getClassid());
}
datasource_country
.joinWith(
cfhb, cfhb
.col("entity2Id")
.equalTo(datasource_country.col("datasourceId")))
.groupByKey(
(MapFunction<Tuple2<DatasourceCountry, EntityEntityRel>, String>) t2 -> t2._2().getEntity1Id(),
Encoders.STRING())
.mapGroups(
(MapGroupsFunction<String, Tuple2<DatasourceCountry, EntityEntityRel>, ResultCountrySet>) (k, it) -> {
ResultCountrySet rcs = new ResultCountrySet();
rcs.setResultId(k);
Set<CountrySbs> set = new HashSet<>();
Set<String> countryCodes = new HashSet<>();
DatasourceCountry first = it.next()._1();
countryCodes.add(first.getCountry().getClassid());
set.add(first.getCountry());
it.forEachRemaining(t2 -> {
if (!countryCodes.contains(t2._1().getCountry().getClassid()))
set.add(t2._1().getCountry());
}); });
a.setCountrySet(countryList); rcs.setCountrySet(new ArrayList<>(set));
return a; return rcs;
}) }, Encoders.bean(ResultCountrySet.class))
.map(couple -> OBJECT_MAPPER.writeValueAsString(couple._2())) .write()
.saveAsTextFile(outputPath, GzipCodec.class); .mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
} }
} }

43
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java
View File

@ -56,12 +56,6 @@ public class SparkCountryPropagationJob {
final String resultClassName = parser.get("resultTableName"); final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName); log.info("resultTableName: {}", resultClassName);
final Boolean saveGraph = Optional
.ofNullable(parser.get("saveGraph"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("saveGraph: {}", saveGraph);
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName); Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
@ -75,8 +69,7 @@ public class SparkCountryPropagationJob {
sourcePath, sourcePath,
preparedInfoPath, preparedInfoPath,
outputPath, outputPath,
resultClazz, resultClazz);
saveGraph);
}); });
} }
@ -85,27 +78,25 @@ public class SparkCountryPropagationJob {
String sourcePath, String sourcePath,
String preparedInfoPath, String preparedInfoPath,
String outputPath, String outputPath,
Class<R> resultClazz, Class<R> resultClazz) {
boolean saveGraph) {
if (saveGraph) { log.info("Reading Graph table from: {}", sourcePath);
log.info("Reading Graph table from: {}", sourcePath); Dataset<R> res = readPath(spark, sourcePath, resultClazz);
Dataset<R> res = readPath(spark, sourcePath, resultClazz);
log.info("Reading prepared info: {}", preparedInfoPath); log.info("Reading prepared info: {}", preparedInfoPath);
Dataset<ResultCountrySet> prepared = spark Dataset<ResultCountrySet> prepared = spark
.read() .read()
.json(preparedInfoPath) .json(preparedInfoPath)
.as(Encoders.bean(ResultCountrySet.class)); .as(Encoders.bean(ResultCountrySet.class));
res
.joinWith(prepared, res.col("id").equalTo(prepared.col("resultId")), "left_outer")
.map(getCountryMergeFn(), Encoders.bean(resultClazz))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
res
.joinWith(prepared, res.col("id").equalTo(prepared.col("resultId")), "left_outer")
.map(getCountryMergeFn(), Encoders.bean(resultClazz))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
}
} }
private static <R extends Result> MapFunction<Tuple2<R, ResultCountrySet>, R> getCountryMergeFn() { private static <R extends Result> MapFunction<Tuple2<R, ResultCountrySet>, R> getCountryMergeFn() {

12
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json
View File

@ -5,18 +5,6 @@
"paramDescription": "the path of the sequencial file to read", "paramDescription": "the path of the sequencial file to read",
"paramRequired": true "paramRequired": true
}, },
{
"paramName":"h",
"paramLongName":"hive_metastore_uris",
"paramDescription": "the hive metastore uris",
"paramRequired": false
},
{
"paramName":"sg",
"paramLongName":"saveGraph",
"paramDescription": "true if the new version of the graph must be saved",
"paramRequired": false
},
{ {
"paramName":"tn", "paramName":"tn",
"paramLongName":"resultTableName", "paramLongName":"resultTableName",

6
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareassoc_parameters.json
View File

@ -5,12 +5,6 @@
"paramDescription": "the path of the sequencial file to read", "paramDescription": "the path of the sequencial file to read",
"paramRequired": true "paramRequired": true
}, },
{
"paramName":"h",
"paramLongName":"hive_metastore_uris",
"paramDescription": "the hive metastore uris",
"paramRequired": true
},
{ {
"paramName": "out", "paramName": "out",
"paramLongName": "outputPath", "paramLongName": "outputPath",

6
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareresultcountry_parameters.json
View File

@ -12,9 +12,9 @@
"paramRequired": true "paramRequired": true
}, },
{ {
"paramName":"h", "paramName":"w",
"paramLongName":"hive_metastore_uris", "paramLongName":"workingPath",
"paramDescription": "the hive metastore uris", "paramDescription": "the working path",
"paramRequired": true "paramRequired": true
}, },
{ {

9
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml
View File

@ -110,7 +110,6 @@
<arg>--sourcePath</arg><arg>${sourcePath}</arg> <arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--whitelist</arg><arg>${whitelist}</arg> <arg>--whitelist</arg><arg>${whitelist}</arg>
<arg>--allowedtypes</arg><arg>${allowedtypes}</arg> <arg>--allowedtypes</arg><arg>${allowedtypes}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo</arg> <arg>--outputPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark> </spark>
<ok to="fork_join_prepare_result_country"/> <ok to="fork_join_prepare_result_country"/>
@ -146,7 +145,7 @@
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg> <arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/publication</arg> <arg>--outputPath</arg><arg>${workingDir}/publication</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--workingPath</arg><arg>${workingDir}/workingP</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg> <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg> <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark> </spark>
@ -176,7 +175,7 @@
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg> <arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/dataset</arg> <arg>--outputPath</arg><arg>${workingDir}/dataset</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--workingPath</arg><arg>${workingDir}/workingD</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg> <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg> <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark> </spark>
@ -206,7 +205,7 @@
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg> <arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg> <arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--workingPath</arg><arg>${workingDir}/workingO</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg> <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg> <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark> </spark>
@ -236,7 +235,7 @@
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg> <arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--outputPath</arg><arg>${workingDir}/software</arg> <arg>--outputPath</arg><arg>${workingDir}/software</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--workingPath</arg><arg>${workingDir}/workingS</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg> <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg> <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark> </spark>

1
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/oozie_app/workflow.xml
View File

@ -173,6 +173,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
--conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--relationPath</arg><arg>${workingDir}/preparedInfo/relation</arg> <arg>--relationPath</arg><arg>${workingDir}/preparedInfo/relation</arg>
<arg>--outputPath</arg><arg>${outputPath}/relation</arg> <arg>--outputPath</arg><arg>${outputPath}/relation</arg>

149
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java
View File

@ -24,6 +24,7 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Country; import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.schema.oaf.Software;
import scala.Tuple2; import scala.Tuple2;
@ -69,17 +70,16 @@ public class CountryPropagationJobTest {
@Test @Test
void testCountryPropagationSoftware() throws Exception { void testCountryPropagationSoftware() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/sample/software") .getResource("/eu/dnetlib/dhp/countrypropagation/graph/software")
.getPath(); .getPath();
final String preparedInfoPath = getClass() final String preparedInfoPath = getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo") .getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo/software")
.getPath(); .getPath();
SparkCountryPropagationJob SparkCountryPropagationJob
.main( .main(
new String[] { new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(), "--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sourcePath, "--sourcePath", sourcePath,
"-saveGraph", "true",
"-resultTableName", Software.class.getCanonicalName(), "-resultTableName", Software.class.getCanonicalName(),
"-outputPath", workingDir.toString() + "/software", "-outputPath", workingDir.toString() + "/software",
"-preparedInfoPath", preparedInfoPath "-preparedInfoPath", preparedInfoPath
@ -91,8 +91,6 @@ public class CountryPropagationJobTest {
.textFile(workingDir.toString() + "/software") .textFile(workingDir.toString() + "/software")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class)); .map(item -> OBJECT_MAPPER.readValue(item, Software.class));
// tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s));
Assertions.assertEquals(10, tmp.count()); Assertions.assertEquals(10, tmp.count());
Dataset<Software> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Software.class)); Dataset<Software> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Software.class));
@ -259,4 +257,145 @@ public class CountryPropagationJobTest {
7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count()); 7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count());
} }
@Test
void testCountryPropagationPublication() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/graph/publication")
.getPath();
final String preparedInfoPath = getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo/publication")
.getPath();
SparkCountryPropagationJob
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sourcePath,
"-resultTableName", Publication.class.getCanonicalName(),
"-outputPath", workingDir.toString() + "/publication",
"-preparedInfoPath", preparedInfoPath
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.textFile(workingDir.toString() + "/publication")
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
Assertions.assertEquals(12, tmp.count());
Assertions.assertEquals(5, tmp.filter(r -> r.getCountry().size() > 0).count());
tmp
.foreach(
r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemeid())));
tmp
.foreach(
r -> r
.getCountry()
.stream()
.forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemename())));
tmp
.foreach(
r -> r
.getCountry()
.stream()
.forEach(c -> Assertions.assertFalse(c.getDataInfo().getDeletedbyinference())));
tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertFalse(c.getDataInfo().getInvisible())));
tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertTrue(c.getDataInfo().getInferred())));
tmp
.foreach(
r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("0.85", c.getDataInfo().getTrust())));
tmp
.foreach(
r -> r
.getCountry()
.stream()
.forEach(c -> Assertions.assertEquals("propagation", c.getDataInfo().getInferenceprovenance())));
tmp
.foreach(
r -> r
.getCountry()
.stream()
.forEach(
c -> Assertions
.assertEquals("country:instrepos", c.getDataInfo().getProvenanceaction().getClassid())));
tmp
.foreach(
r -> r
.getCountry()
.stream()
.forEach(
c -> Assertions
.assertEquals(
"dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemeid())));
tmp
.foreach(
r -> r
.getCountry()
.stream()
.forEach(
c -> Assertions
.assertEquals(
"dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemename())));
List<Country> countries = tmp
.filter(r -> r.getId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072"))
.collect()
.get(0)
.getCountry();
Assertions.assertEquals(1, countries.size());
Assertions.assertEquals("NL", countries.get(0).getClassid());
Assertions.assertEquals("Netherlands", countries.get(0).getClassname());
countries = tmp
.filter(r -> r.getId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b"))
.collect()
.get(0)
.getCountry();
Assertions.assertEquals(1, countries.size());
Assertions.assertEquals("NL", countries.get(0).getClassid());
Assertions.assertEquals("Netherlands", countries.get(0).getClassname());
countries = tmp
.filter(r -> r.getId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6"))
.collect()
.get(0)
.getCountry();
Assertions.assertEquals(2, countries.size());
Assertions
.assertTrue(
countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
countries = tmp
.filter(r -> r.getId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df"))
.collect()
.get(0)
.getCountry();
Assertions.assertEquals(2, countries.size());
Assertions
.assertTrue(
countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
countries
.stream()
.anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands")));
countries = tmp
.filter(r -> r.getId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088"))
.collect()
.get(0)
.getCountry();
Assertions.assertEquals(2, countries.size());
Assertions
.assertTrue(
countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
}
} }

176
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java Normal file
View File

@ -0,0 +1,176 @@
package eu.dnetlib.dhp.countrypropagation;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
public class DatasourceCountryPreparationTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(DatasourceCountryPreparationTest.class.getSimpleName());
SparkConf conf = new SparkConf();
conf.setAppName(DatasourceCountryPreparationTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(DatasourceCountryPreparationTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void testPrepareDatasourceCountry() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/graph")
.getPath();
PrepareDatasourceCountryAssociation
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sourcePath,
"--outputPath", workingDir.toString() + "/datasourceCountry",
"--allowedtypes", "pubsrepository::institutional",
"--whitelist",
"10|openaire____::3795d6478e30e2c9f787d427ff160944;10|opendoar____::16e6a3326dd7d868cbc926602a61e4d0;10|eurocrisdris::fe4903425d9040f680d8610d9079ea14;10|openaire____::5b76240cc27a58c6f7ceef7d8c36660e;10|openaire____::172bbccecf8fca44ab6a6653e84cb92a;10|openaire____::149c6590f8a06b46314eed77bfca693f;10|eurocrisdris::a6026877c1a174d60f81fd71f62df1c1;10|openaire____::4692342f0992d91f9e705c26959f09e0;10|openaire____::8d529dbb05ec0284662b391789e8ae2a;10|openaire____::345c9d171ef3c5d706d08041d506428c;10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0;10|opendoar____::7a614fd06c325499f1680b9896beedeb;10|opendoar____::1ee3dfcd8a0645a25a35977997223d22;10|opendoar____::d296c101daa88a51f6ca8cfc1ac79b50;10|opendoar____::798ed7d4ee7138d49b8828958048130a;10|openaire____::c9d2209ecc4d45ba7b4ca7597acb88a2;10|eurocrisdris::c49e0fe4b9ba7b7fab717d1f0f0a674d;10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539;10|eurocrisdris::432ca599953ff50cd4eeffe22faf3e48"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<DatasourceCountry> tmp = sc
.textFile(workingDir.toString() + "/datasourceCountry")
.map(item -> OBJECT_MAPPER.readValue(item, DatasourceCountry.class));
Assertions.assertEquals(3, tmp.count());
Assertions
.assertEquals(
1, tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14"))
.count());
Assertions
.assertEquals(
1, tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280"))
.count());
Assertions
.assertEquals(
1, tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539"))
.count());
Assertions
.assertEquals(
"NL", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14"))
.collect()
.get(0)
.getCountry()
.getClassid());
Assertions
.assertEquals(
"Netherlands", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14"))
.collect()
.get(0)
.getCountry()
.getClassname());
Assertions
.assertEquals(
"IT", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280"))
.collect()
.get(0)
.getCountry()
.getClassid());
Assertions
.assertEquals(
"Italy", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280"))
.collect()
.get(0)
.getCountry()
.getClassname());
Assertions
.assertEquals(
"FR", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539"))
.collect()
.get(0)
.getCountry()
.getClassid());
Assertions
.assertEquals(
"France", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539"))
.collect()
.get(0)
.getCountry()
.getClassname());
tmp.foreach(e -> System.out.println(OBJECT_MAPPER.writeValueAsString(e)));
}
}

158
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/ResultCountryPreparationTest.java Normal file
View File

@ -0,0 +1,158 @@
package eu.dnetlib.dhp.countrypropagation;
import static eu.dnetlib.dhp.PropagationConstant.isSparkSessionManaged;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Publication;
public class ResultCountryPreparationTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(ResultCountryPreparationTest.class.getSimpleName());
SparkConf conf = new SparkConf();
conf.setAppName(ResultCountryPreparationTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(ResultCountryPreparationTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void testPrepareResultCountry() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/graph/publication")
.getPath();
final String preparedInfoPath = getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/datasourcecountry")
.getPath();
PrepareResultCountrySet
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--workingPath", workingDir.toString() + "/working",
"--sourcePath", sourcePath,
"--outputPath", workingDir.toString() + "/resultCountry",
"--preparedInfoPath", preparedInfoPath,
"--resultTableName", Publication.class.getCanonicalName()
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<ResultCountrySet> tmp = sc
.textFile(workingDir.toString() + "/resultCountry")
.map(item -> OBJECT_MAPPER.readValue(item, ResultCountrySet.class));
Assertions.assertEquals(5, tmp.count());
ResultCountrySet rc = tmp
.filter(r -> r.getResultId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072"))
.collect()
.get(0);
Assertions.assertEquals(1, rc.getCountrySet().size());
Assertions.assertEquals("NL", rc.getCountrySet().get(0).getClassid());
Assertions.assertEquals("Netherlands", rc.getCountrySet().get(0).getClassname());
rc = tmp
.filter(r -> r.getResultId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b"))
.collect()
.get(0);
Assertions.assertEquals(1, rc.getCountrySet().size());
Assertions.assertEquals("NL", rc.getCountrySet().get(0).getClassid());
Assertions.assertEquals("Netherlands", rc.getCountrySet().get(0).getClassname());
rc = tmp
.filter(r -> r.getResultId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6"))
.collect()
.get(0);
Assertions.assertEquals(2, rc.getCountrySet().size());
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
rc = tmp
.filter(r -> r.getResultId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df"))
.collect()
.get(0);
Assertions.assertEquals(2, rc.getCountrySet().size());
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands")));
rc = tmp
.filter(r -> r.getResultId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088"))
.collect()
.get(0);
Assertions.assertEquals(2, rc.getCountrySet().size());
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
}
}

3
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/datasourcecountry/datasourcecountry Normal file
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@ -0,0 +1,3 @@
{"dataSourceId":"10|eurocrisdris::fe4903425d9040f680d8610d9079ea14","country":{"classid":"NL","classname":"Netherlands"}}
{"dataSourceId":"10|opendoar____::f0dd4a99fba6075a9494772b58f95280","country":{"classid":"IT","classname":"Italy"}}
{"dataSourceId":"10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539","country":{"classid":"FR","classname":"France"}}

11
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/datasource/datasource.json Normal file
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@ -0,0 +1,11 @@
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","subRelType":"affiliation","target":"50|dedup_wf_001::0a1cdf269375d32ce341fdeb0e92dfa8","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0a1cdf269375d32ce341fdeb0e92dfa8","subRelType":"affiliation","target":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|pending_org_::a50fdd7f7e77b74ea2b16823151c391a","subRelType":"affiliation","target":"50|dedup_wf_001::0ab92bed024ee6883c7a1244722e5eec","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0ab92bed024ee6883c7a1244722e5eec","subRelType":"affiliation","target":"20|pending_org_::a50fdd7f7e77b74ea2b16823151c391a","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|openorgs____::64badd35233ba2cd4946368ef2f4cf57","subRelType":"affiliation","target":"50|dedup_wf_001::0ca26c736ad4d15b3d5ee90a4d7853e1","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0ca26c736ad4d15b3d5ee90a4d7853e1","subRelType":"affiliation","target":"20|openorgs____::64badd35233ba2cd4946368ef2f4cf57","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|pending_org_::a50fdd7f7e77b74ea2b16823151c391a","subRelType":"affiliation","target":"50|dedup_wf_001::0ef8dfab3927cb4d69df0d3113f05a42","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0ef8dfab3927cb4d69df0d3113f05a42","subRelType":"affiliation","target":"20|pending_org_::a50fdd7f7e77b74ea2b16823151c391a","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","subRelType":"affiliation","target":"50|dedup_wf_001::0f488ad00253126c14a21abe6b2d406c","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0f488ad00253126c14a21abe6b2d406c","subRelType":"affiliation","target":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","subRelType":"affiliation","target":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","subRelType":"affiliation","target":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","validated":false}

0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/sample/software/software_10.json.gz → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/software/software_10.json.gz
View File

5
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/publication/resultCountrySet Normal file
View File

@ -0,0 +1,5 @@
{"resultId":"50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b","countrySet":[{"classid":"NL","classname":"Netherlands"}]}
{"resultId":"50|355e65625b88::54a1c76f520bb2c8da27d12e42891088","countrySet":[{"classid":"IT","classname":"Italy"},{"classid":"FR","classname":"France"}]}
{"resultId":"50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072","countrySet":[{"classid":"NL","classname":"Netherlands"}]}
{"resultId":"50|355e65625b88::74009c567c81b4aa55c813db658734df","countrySet":[{"classid":"NL","classname":"Netherlands"},{"classid":"IT","classname":"Italy"}]}
{"resultId":"50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6","countrySet":[{"classid":"IT","classname":"Italy"},{"classid":"FR","classname":"France"}]}

0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/preparedInfo.json.gz → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/software/preparedInfo.json.gz
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137
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/ExtractAndMapDoajJson.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.oa.graph.hostedbymap; package eu.dnetlib.dhp.oa.graph.hostedbymap;
import static eu.dnetlib.dhp.common.collection.DecompressTarGz.doExtract; import static eu.dnetlib.dhp.common.collection.DecompressTarGz.doExtract;
@ -27,90 +28,90 @@ import eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj.DOAJEntry;
public class ExtractAndMapDoajJson { public class ExtractAndMapDoajJson {
private static final Logger log = LoggerFactory.getLogger(ExtractAndMapDoajJson.class); private static final Logger log = LoggerFactory.getLogger(ExtractAndMapDoajJson.class);
public static void main(final String[] args) throws Exception { public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser( final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils IOUtils
.toString( .toString(
Objects Objects
.requireNonNull( .requireNonNull(
ExtractAndMapDoajJson.class ExtractAndMapDoajJson.class
.getResourceAsStream( .getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/hostedbymap/download_json_parameters.json")))); "/eu/dnetlib/dhp/oa/graph/hostedbymap/download_json_parameters.json"))));
parser.parseArgument(args); parser.parseArgument(args);
final String compressedInput = parser.get("compressedFile"); final String compressedInput = parser.get("compressedFile");
log.info("compressedInput {}", compressedInput); log.info("compressedInput {}", compressedInput);
final String hdfsNameNode = parser.get("hdfsNameNode"); final String hdfsNameNode = parser.get("hdfsNameNode");
log.info("hdfsNameNode {}", hdfsNameNode); log.info("hdfsNameNode {}", hdfsNameNode);
final String outputPath = parser.get("outputPath"); final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath); log.info("outputPath {}", outputPath);
final String workingPath = parser.get("workingPath"); final String workingPath = parser.get("workingPath");
log.info("workingPath {}", workingPath); log.info("workingPath {}", workingPath);
Configuration conf = new Configuration(); Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode); conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fs = FileSystem.get(conf); FileSystem fs = FileSystem.get(conf);
CompressionCodecFactory factory = new CompressionCodecFactory(conf); CompressionCodecFactory factory = new CompressionCodecFactory(conf);
CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec"); CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec");
doExtract(fs, workingPath, compressedInput); doExtract(fs, workingPath, compressedInput);
doMap(fs, workingPath, outputPath, codec); doMap(fs, workingPath, outputPath, codec);
} }
private static void doMap(FileSystem fs, String workingPath, String outputPath, CompressionCodec codec) private static void doMap(FileSystem fs, String workingPath, String outputPath, CompressionCodec codec)
throws IOException { throws IOException {
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fs RemoteIterator<LocatedFileStatus> fileStatusListIterator = fs
.listFiles( .listFiles(
new Path(workingPath), true); new Path(workingPath), true);
Path hdfsWritePath = new Path(outputPath); Path hdfsWritePath = new Path(outputPath);
if (fs.exists(hdfsWritePath)) { if (fs.exists(hdfsWritePath)) {
fs.delete(hdfsWritePath, true); fs.delete(hdfsWritePath, true);
} }
try ( try (
FSDataOutputStream out = fs FSDataOutputStream out = fs
.create(hdfsWritePath); .create(hdfsWritePath);
PrintWriter writer = new PrintWriter(new BufferedOutputStream(out))) { PrintWriter writer = new PrintWriter(new BufferedOutputStream(out))) {
while (fileStatusListIterator.hasNext()) { while (fileStatusListIterator.hasNext()) {
Path path = fileStatusListIterator.next().getPath(); Path path = fileStatusListIterator.next().getPath();
if (!fs.isDirectory(path)) { if (!fs.isDirectory(path)) {
FSDataInputStream is = fs.open(path); FSDataInputStream is = fs.open(path);
CompressionInputStream compressionInputStream = codec.createInputStream(is); CompressionInputStream compressionInputStream = codec.createInputStream(is);
DOAJEntry[] doajEntries = new ObjectMapper().readValue(compressionInputStream, DOAJEntry[].class); DOAJEntry[] doajEntries = new ObjectMapper().readValue(compressionInputStream, DOAJEntry[].class);
Arrays.stream(doajEntries).forEach(doaj -> { Arrays.stream(doajEntries).forEach(doaj -> {
try { try {
writer.println(new ObjectMapper().writeValueAsString(getDoajModel(doaj))); writer.println(new ObjectMapper().writeValueAsString(getDoajModel(doaj)));
} catch (JsonProcessingException e) { } catch (JsonProcessingException e) {
e.printStackTrace(); e.printStackTrace();
} }
}); });
} }
} }
} }
} }
@NotNull @NotNull
public static DOAJModel getDoajModel(DOAJEntry doaj) { public static DOAJModel getDoajModel(DOAJEntry doaj) {
DOAJModel doajModel = new DOAJModel(); DOAJModel doajModel = new DOAJModel();
doajModel.setOaStart(doaj.getBibjson().getOa_start()); doajModel.setOaStart(doaj.getBibjson().getOa_start());
doajModel.setEissn(doaj.getBibjson().getEissn()); doajModel.setEissn(doaj.getBibjson().getEissn());
doajModel.setIssn(doaj.getBibjson().getPissn()); doajModel.setIssn(doaj.getBibjson().getPissn());
doajModel.setJournalTitle(doaj.getBibjson().getTitle()); doajModel.setJournalTitle(doaj.getBibjson().getTitle());
doajModel.setReviewProcess(doaj.getBibjson().getEditorial().getReview_process()); doajModel.setReviewProcess(doaj.getBibjson().getEditorial().getReview_process());
return doajModel; return doajModel;
} }
} }

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/doaj/BibJson.java
View File

@ -4,8 +4,6 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap.model.doaj;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import com.fasterxml.jackson.annotation.JsonIgnore;
public class BibJson implements Serializable { public class BibJson implements Serializable {
private Editorial editorial; private Editorial editorial;
private PidScheme pid_scheme; private PidScheme pid_scheme;

3
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
View File

@ -309,6 +309,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
ds.setThematic(rs.getBoolean("thematic")); ds.setThematic(rs.getBoolean("thematic"));
ds.setKnowledgegraph(rs.getBoolean("knowledgegraph")); ds.setKnowledgegraph(rs.getBoolean("knowledgegraph"));
ds.setContentpolicies(prepareListOfQualifiers(rs.getArray("contentpolicies"))); ds.setContentpolicies(prepareListOfQualifiers(rs.getArray("contentpolicies")));
ds.setConsenttermsofuse(rs.getBoolean("consenttermsofuse"));
ds.setFulltextdownload(rs.getBoolean("fulltextdownload"));
ds.setConsenttermsofusedate(rs.getDate("consenttermsofusedate").toString());
return Arrays.asList(ds); return Arrays.asList(ds);
} catch (final Exception e) { } catch (final Exception e) {

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
View File

@ -25,7 +25,7 @@ import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
public class OdfToOafMapper extends AbstractMdRecordToOafMapper { public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
public static final String HTTP_DX_DOI_PREIFX = "http://dx.doi.org/"; public static final String HTTP_DX_DOI_PREIFX = "https://dx.doi.org/";
public OdfToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId, public OdfToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId,
final boolean forceOrginalId) { final boolean forceOrginalId) {

27
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/download_json_parameters.json Normal file
View File

@ -0,0 +1,27 @@
[
{
"paramName":"op",
"paramLongName":"outputPath",
"paramDescription": "the output json file produced by the CSV downlaod procedure",
"paramRequired": true
},
{
"paramName": "hnn",
"paramLongName": "hdfsNameNode",
"paramDescription": "the path used to store the HostedByMap",
"paramRequired": true
},{
"paramName": "cf",
"paramLongName": "compressedFile",
"paramDescription": "the path used to store the HostedByMap",
"paramRequired": true
},{
"paramName":"wp",
"paramLongName":"workingPath",
"paramDescription": "the output json file produced by the CSV downlaod procedure",
"paramRequired": true
}
]

3
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/download.sh Normal file
View File

@ -0,0 +1,3 @@
#!/bin/bash
curl -LSs $1 | hdfs dfs -put - $2/$3
curl -LSs http://api.crossref.org/works/10.1099/jgv.0.001453 > prova.txt

2
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml
View File

@ -92,7 +92,7 @@
<action name="download_gold"> <action name="download_gold">
<java> <java>
<main-class>eu.dnetlib.dhp.oa.graph.hostedbymap.DownloadCSV2</main-class> <main-class>eu.dnetlib.dhp.oa.graph.hostedbymap.DownloadCSV</main-class>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg> <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
<arg>--fileURL</arg><arg>${unibiFileURL}</arg> <arg>--fileURL</arg><arg>${unibiFileURL}</arg>
<arg>--tmpFile</arg><arg>/tmp/unibi_gold_replaced.csv</arg> <arg>--tmpFile</arg><arg>/tmp/unibi_gold_replaced.csv</arg>

3
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql
View File

@ -89,6 +89,9 @@ SELECT
d.issn AS issnPrinted, d.issn AS issnPrinted,
d.eissn AS issnOnline, d.eissn AS issnOnline,
d.lissn AS issnLinking, d.lissn AS issnLinking,
d.consenttermsofuse AS consenttermsofuse,
d.fulltextdownload AS fulltextdownload,
d.consenttermsofusedate AS consenttermsofusedate,
de.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, de.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction,
de.thematic AS thematic, de.thematic AS thematic,
de.knowledge_graph AS knowledgegraph, de.knowledge_graph AS knowledgegraph,

11
dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala
View File

@ -173,7 +173,16 @@ object SparkProduceHostedByMap {
} }
def doajToHostedbyItemType(doaj: DOAJModel): HostedByItemType = { def doajToHostedbyItemType(doaj: DOAJModel): HostedByItemType = {
if (doaj.getOaStart == null) {
return getHostedByItemType(
Constants.DOAJ,
doaj.getJournalTitle,
doaj.getIssn,
doaj.getEissn,
"",
true
)
}
return getHostedByItemType( return getHostedByItemType(
Constants.DOAJ, Constants.DOAJ,
doaj.getJournalTitle, doaj.getJournalTitle,

3
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java
View File

@ -100,6 +100,9 @@ public class MigrateDbEntitiesApplicationTest {
assertEquals("Journal article", ds.getContentpolicies().get(0).getClassid()); assertEquals("Journal article", ds.getContentpolicies().get(0).getClassid());
assertEquals("eosc:contentpolicies", ds.getContentpolicies().get(0).getSchemeid()); assertEquals("eosc:contentpolicies", ds.getContentpolicies().get(0).getSchemeid());
assertEquals(true, ds.getConsenttermsofuse());
assertEquals(true, ds.getFulltextdownload());
assertEquals("2022-03-11", ds.getConsenttermsofusedate());
} }
@Test @Test

15
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json
View File

@ -268,5 +268,20 @@
"value": [ "value": [
"Journal article@@@eosc:contentpolicies" "Journal article@@@eosc:contentpolicies"
] ]
},
{
"field": "consenttermsofuse",
"type": "boolean",
"value": true
},
{
"field": "fulltextdownload",
"type": "boolean",
"value": true
},
{
"field": "consenttermsofusedate",
"type": "date",
"value": "2022-03-11"
} }
] ]

13
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/XmlInstance.java
View File

@ -12,6 +12,7 @@ import scala.Serializable;
public class XmlInstance implements Serializable { public class XmlInstance implements Serializable {
public static final AccessRight UNKNOWN_ACCESS_RIGHT; public static final AccessRight UNKNOWN_ACCESS_RIGHT;
public static final Qualifier UNKNOWN_REVIEW_LEVEL;
static { static {
UNKNOWN_ACCESS_RIGHT = new AccessRight(); UNKNOWN_ACCESS_RIGHT = new AccessRight();
@ -19,6 +20,12 @@ public class XmlInstance implements Serializable {
UNKNOWN_ACCESS_RIGHT.setClassname(ModelConstants.UNKNOWN); UNKNOWN_ACCESS_RIGHT.setClassname(ModelConstants.UNKNOWN);
UNKNOWN_ACCESS_RIGHT.setSchemeid(ModelConstants.DNET_ACCESS_MODES); UNKNOWN_ACCESS_RIGHT.setSchemeid(ModelConstants.DNET_ACCESS_MODES);
UNKNOWN_ACCESS_RIGHT.setSchemename(ModelConstants.DNET_ACCESS_MODES); UNKNOWN_ACCESS_RIGHT.setSchemename(ModelConstants.DNET_ACCESS_MODES);
UNKNOWN_REVIEW_LEVEL = new Qualifier();
UNKNOWN_REVIEW_LEVEL.setClassid("0000");
UNKNOWN_REVIEW_LEVEL.setClassname(ModelConstants.UNKNOWN);
UNKNOWN_ACCESS_RIGHT.setSchemeid(ModelConstants.DNET_REVIEW_LEVELS);
UNKNOWN_REVIEW_LEVEL.setSchemename(ModelConstants.DNET_REVIEW_LEVELS);
} }
private String url; private String url;
@ -50,7 +57,7 @@ public class XmlInstance implements Serializable {
// typed results // typed results
private String processingchargecurrency; private String processingchargecurrency;
private Set<Qualifier> refereed = Sets.newHashSet();; // peer-review status private Qualifier refereed; // peer-review status
public String getUrl() { public String getUrl() {
return url; return url;
@ -148,11 +155,11 @@ public class XmlInstance implements Serializable {
this.processingchargecurrency = processingchargecurrency; this.processingchargecurrency = processingchargecurrency;
} }
public Set<Qualifier> getRefereed() { public Qualifier getRefereed() {
return refereed; return refereed;
} }
public void setRefereed(Set<Qualifier> refereed) { public void setRefereed(Qualifier refereed) {
this.refereed = refereed; this.refereed = refereed;
} }
} }

20
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
View File

@ -31,6 +31,7 @@ import org.dom4j.Node;
import org.dom4j.io.OutputFormat; import org.dom4j.io.OutputFormat;
import org.dom4j.io.SAXReader; import org.dom4j.io.SAXReader;
import org.dom4j.io.XMLWriter; import org.dom4j.io.XMLWriter;
import org.json4s.Xml;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.base.Joiner; import com.google.common.base.Joiner;
@ -1208,14 +1209,8 @@ public class XmlRecordFactory implements Serializable {
if (instance.getRefereed() != null) { if (instance.getRefereed() != null) {
fields fields
.addAll( .add(
instance XmlSerializationUtils.mapQualifier("refereed", instance.getRefereed()));
.getRefereed()
.stream()
.filter(Objects::nonNull)
.filter(r -> !r.isBlank())
.map(r -> XmlSerializationUtils.mapQualifier("refereed", r))
.collect(Collectors.toList()));
} }
if (instance.getProcessingchargeamount() != null if (instance.getProcessingchargeamount() != null
&& isNotBlank(instance.getProcessingchargeamount())) { && isNotBlank(instance.getProcessingchargeamount())) {
@ -1359,13 +1354,20 @@ public class XmlRecordFactory implements Serializable {
.map(Instance::getAccessright) .map(Instance::getAccessright)
.min(new AccessRightComparator<AccessRight>()) .min(new AccessRightComparator<AccessRight>())
.orElse(XmlInstance.UNKNOWN_ACCESS_RIGHT)); .orElse(XmlInstance.UNKNOWN_ACCESS_RIGHT));
instance
.setRefereed(
instances
.stream()
.map(Pair::getValue)
.map(i -> Optional.ofNullable(i.getRefereed()).orElse(XmlInstance.UNKNOWN_REVIEW_LEVEL))
.min(new RefereedComparator())
.orElse(XmlInstance.UNKNOWN_REVIEW_LEVEL));
instances.forEach(p -> { instances.forEach(p -> {
final Instance i = p.getRight(); final Instance i = p.getRight();
instance.getCollectedfrom().add(i.getCollectedfrom()); instance.getCollectedfrom().add(i.getCollectedfrom());
instance.getHostedby().add(i.getHostedby()); instance.getHostedby().add(i.getHostedby());
instance.getInstancetype().add(i.getInstancetype()); instance.getInstancetype().add(i.getInstancetype());
instance.getRefereed().add(i.getRefereed());
instance instance
.setProcessingchargeamount( .setProcessingchargeamount(
Optional.ofNullable(i.getProcessingchargeamount()).map(apc -> apc.getValue()).orElse(null)); Optional.ofNullable(i.getProcessingchargeamount()).map(apc -> apc.getValue()).orElse(null));

2
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
View File

@ -66,7 +66,7 @@ public class XmlRecordFactoryTest {
assertEquals("doi", doc.valueOf("//instance/alternateidentifier/@classid")); assertEquals("doi", doc.valueOf("//instance/alternateidentifier/@classid"));
assertEquals("10.5689/LIB.2018.2853550", doc.valueOf("//instance/alternateidentifier/text()")); assertEquals("10.5689/LIB.2018.2853550", doc.valueOf("//instance/alternateidentifier/text()"));
assertEquals(3, doc.selectNodes("//instance").size()); assertEquals(2, doc.selectNodes("//instance").size());
assertEquals("1721.47", doc.valueOf("//processingchargeamount/text()")); assertEquals("1721.47", doc.valueOf("//processingchargeamount/text()"));
assertEquals("EUR", doc.valueOf("//processingchargecurrency/text()")); assertEquals("EUR", doc.valueOf("//processingchargecurrency/text()"));

26
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json
View File

@ -453,6 +453,12 @@
"schemeid": "dnet:dataCite_resource", "schemeid": "dnet:dataCite_resource",
"schemename": "dnet:dataCite_resource" "schemename": "dnet:dataCite_resource"
}, },
"refereed": {
"classid": "0001",
"classname": "peerReviewed",
"schemeid": "dnet:review_levels",
"schemename": "dnet:review_levels"
},
"license": { "license": {
"dataInfo": { "dataInfo": {
"deletedbyinference": false, "deletedbyinference": false,
@ -585,6 +591,12 @@
"schemeid": "dnet:dataCite_resource", "schemeid": "dnet:dataCite_resource",
"schemename": "dnet:dataCite_resource" "schemename": "dnet:dataCite_resource"
}, },
"refereed": {
"classid": "0000",
"classname": "UNKNOWN",
"schemeid": "dnet:review_levels",
"schemename": "dnet:review_levels"
},
"license": { "license": {
"dataInfo": { "dataInfo": {
"deletedbyinference": false, "deletedbyinference": false,
@ -717,6 +729,12 @@
"schemeid": "dnet:dataCite_resource", "schemeid": "dnet:dataCite_resource",
"schemename": "dnet:dataCite_resource" "schemename": "dnet:dataCite_resource"
}, },
"refereed": {
"classid": "0002",
"classname": "nonPeerReviewed",
"schemeid": "dnet:review_levels",
"schemename": "dnet:review_levels"
},
"license": { "license": {
"dataInfo": { "dataInfo": {
"deletedbyinference": false, "deletedbyinference": false,
@ -849,6 +867,12 @@
"schemeid": "dnet:dataCite_resource", "schemeid": "dnet:dataCite_resource",
"schemename": "dnet:dataCite_resource" "schemename": "dnet:dataCite_resource"
}, },
"refereed": {
"classid": "0001",
"classname": "peerReviewed",
"schemeid": "dnet:review_levels",
"schemename": "dnet:review_levels"
},
"license": { "license": {
"dataInfo": { "dataInfo": {
"deletedbyinference": false, "deletedbyinference": false,
@ -866,7 +890,7 @@
"value": "" "value": ""
}, },
"url": [ "url": [
"http://dx.doi.org/10.1109/TED.2018.2853552", "http://dx.doi.org/10.1109/TED.2018.2853551",
"http://dx.doi.org/10.1109/TED.2018.2853554" "http://dx.doi.org/10.1109/TED.2018.2853554"
] ]
}, },

5
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql
View File

@ -49,8 +49,5 @@ select * from openaire_prod_usage_stats.views_stats;
-- Creation date of the database -- Creation date of the database
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
create table ${stats_db_name}.creation_date as create table ${stats_db_name}.creation_date STORED AS PARQUET as
select date_format(current_date(), 'dd-MM-yyyy') as date; select date_format(current_date(), 'dd-MM-yyyy') as date;
--
-- ANALYZE TABLE ${stats_db_name}.creation_date COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.creation_date COMPUTE STATISTICS FOR COLUMNS;

5
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
View File

@ -113,7 +113,4 @@ FROM ${stats_db_name}.result_projects,
${stats_db_name}.project ${stats_db_name}.project
WHERE result_projects.id = result.id WHERE result_projects.id = result.id
AND result.type = 'publication' AND result.type = 'publication'
AND project.id = result_projects.project; AND project.id = result_projects.project;
-- ANALYZE TABLE ${stats_db_name}.project COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.project COMPUTE STATISTICS FOR COLUMNS;

10
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql
View File

@ -5,7 +5,7 @@
-- Sources related tables/views -- Sources related tables/views
------------------------------------------------------ ------------------------------------------------------
------------------------------------------------------ ------------------------------------------------------
CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_sources as CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_sources STORED AS PARQUET as
SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource
FROM ( FROM (
SELECT substr(p.id, 4) as id, substr(datasource, 4) as datasource SELECT substr(p.id, 4) as id, substr(datasource, 4) as datasource
@ -16,7 +16,7 @@ LEFT OUTER JOIN
from ${openaire_db_name}.datasource d from ${openaire_db_name}.datasource d
WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id;
CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_sources as CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_sources STORED AS PARQUET as
SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource
FROM ( FROM (
SELECT substr(p.id, 4) as id, substr(datasource, 4) as datasource SELECT substr(p.id, 4) as id, substr(datasource, 4) as datasource
@ -27,7 +27,7 @@ LEFT OUTER JOIN
from ${openaire_db_name}.datasource d from ${openaire_db_name}.datasource d
WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id;
CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_sources as CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_sources STORED AS PARQUET as
SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource
FROM ( FROM (
SELECT substr(p.id, 4) as id, substr(datasource, 4) as datasource SELECT substr(p.id, 4) as id, substr(datasource, 4) as datasource
@ -38,7 +38,7 @@ LEFT OUTER JOIN
from ${openaire_db_name}.datasource d from ${openaire_db_name}.datasource d
WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id;
CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_sources as CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_sources STORED AS PARQUET as
SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource
FROM ( FROM (
SELECT substr(p.id, 4) as id, substr(datasource, 4) as datasource SELECT substr(p.id, 4) as id, substr(datasource, 4) as datasource
@ -59,7 +59,7 @@ UNION ALL
SELECT * FROM ${stats_db_name}.otherresearchproduct_sources; SELECT * FROM ${stats_db_name}.otherresearchproduct_sources;
create table ${stats_db_name}.result_orcid as create table ${stats_db_name}.result_orcid STORED AS PARQUET as
select distinct res.id, regexp_replace(res.orcid, 'http://orcid.org/' ,'') as orcid select distinct res.id, regexp_replace(res.orcid, 'http://orcid.org/' ,'') as orcid
from ( from (
SELECT substr(res.id, 4) as id, auth_pid.value as orcid SELECT substr(res.id, 4) as id, auth_pid.value as orcid

27
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
View File

@ -5,22 +5,22 @@
-- Licences related tables/views -- Licences related tables/views
------------------------------------------------------ ------------------------------------------------------
------------------------------------------------------ ------------------------------------------------------
CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_licenses AS CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_licenses STORED AS PARQUET AS
SELECT substr(p.id, 4) as id, licenses.value as type SELECT substr(p.id, 4) as id, licenses.value as type
from ${openaire_db_name}.publication p LATERAL VIEW explode(p.instance.license) instances as licenses from ${openaire_db_name}.publication p LATERAL VIEW explode(p.instance.license) instances as licenses
where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE;
CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_licenses AS CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_licenses STORED AS PARQUET AS
SELECT substr(p.id, 4) as id, licenses.value as type SELECT substr(p.id, 4) as id, licenses.value as type
from ${openaire_db_name}.dataset p LATERAL VIEW explode(p.instance.license) instances as licenses from ${openaire_db_name}.dataset p LATERAL VIEW explode(p.instance.license) instances as licenses
where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE;
CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_licenses AS CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_licenses STORED AS PARQUET AS
SELECT substr(p.id, 4) as id, licenses.value as type SELECT substr(p.id, 4) as id, licenses.value as type
from ${openaire_db_name}.software p LATERAL VIEW explode(p.instance.license) instances as licenses from ${openaire_db_name}.software p LATERAL VIEW explode(p.instance.license) instances as licenses
where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE;
CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_licenses AS CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_licenses STORED AS PARQUET AS
SELECT substr(p.id, 4) as id, licenses.value as type SELECT substr(p.id, 4) as id, licenses.value as type
from ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.license) instances as licenses from ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.license) instances as licenses
where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE;
@ -34,11 +34,11 @@ SELECT * FROM ${stats_db_name}.software_licenses
UNION ALL UNION ALL
SELECT * FROM ${stats_db_name}.otherresearchproduct_licenses; SELECT * FROM ${stats_db_name}.otherresearchproduct_licenses;
CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization_pids AS CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization_pids STORED AS PARQUET AS
select substr(o.id, 4) as id, ppid.qualifier.classname as type, ppid.value as pid select substr(o.id, 4) as id, ppid.qualifier.classname as type, ppid.value as pid
from ${openaire_db_name}.organization o lateral view explode(o.pid) pids as ppid; from ${openaire_db_name}.organization o lateral view explode(o.pid) pids as ppid;
CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization_sources as CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization_sources STORED AS PARQUET as
SELECT o.id, case when d.id is null then 'other' else o.datasource end as datasource SELECT o.id, case when d.id is null then 'other' else o.datasource end as datasource
FROM ( FROM (
SELECT substr(o.id, 4) as id, substr(instances.instance.key, 4) as datasource SELECT substr(o.id, 4) as id, substr(instances.instance.key, 4) as datasource
@ -46,17 +46,4 @@ FROM (
LEFT OUTER JOIN ( LEFT OUTER JOIN (
SELECT substr(d.id, 4) id SELECT substr(d.id, 4) id
from ${openaire_db_name}.datasource d from ${openaire_db_name}.datasource d
WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on o.datasource = d.id; WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on o.datasource = d.id;
-- ANALYZE TABLE ${stats_db_name}.publication_licenses COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.publication_licenses COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.dataset_licenses COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.dataset_licenses COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.software_licenses COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.software_licenses COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_licenses COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_licenses COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.organization_pids COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.organization_pids COMPUTE STATISTICS FOR COLUMNS;
-- ANALYZE TABLE ${stats_db_name}.organization_sources COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.organization_sources COMPUTE STATISTICS FOR COLUMNS;

8
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql
View File

@ -6,22 +6,22 @@
------------------------------------------------------ ------------------------------------------------------
------------------------------------------------------ ------------------------------------------------------
CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_refereed as CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_refereed STORED AS PARQUET as
select substr(r.id, 4) as id, inst.refereed.classname as refereed select substr(r.id, 4) as id, inst.refereed.classname as refereed
from ${openaire_db_name}.publication r lateral view explode(r.instance) instances as inst from ${openaire_db_name}.publication r lateral view explode(r.instance) instances as inst
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE;
CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_refereed as CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_refereed STORED AS PARQUET as
select substr(r.id, 4) as id, inst.refereed.classname as refereed select substr(r.id, 4) as id, inst.refereed.classname as refereed
from ${openaire_db_name}.dataset r lateral view explode(r.instance) instances as inst from ${openaire_db_name}.dataset r lateral view explode(r.instance) instances as inst
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE;
CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_refereed as CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_refereed STORED AS PARQUET as
select substr(r.id, 4) as id, inst.refereed.classname as refereed select substr(r.id, 4) as id, inst.refereed.classname as refereed
from ${openaire_db_name}.software r lateral view explode(r.instance) instances as inst from ${openaire_db_name}.software r lateral view explode(r.instance) instances as inst
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE;
CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_refereed as CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_refereed STORED AS PARQUET as
select substr(r.id, 4) as id, inst.refereed.classname as refereed select substr(r.id, 4) as id, inst.refereed.classname as refereed
from ${openaire_db_name}.otherresearchproduct r lateral view explode(r.instance) instances as inst from ${openaire_db_name}.otherresearchproduct r lateral view explode(r.instance) instances as inst
where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE; where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE;

6
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql
View File

@ -1,21 +1,21 @@
------------------------------------------- -------------------------------------------
--- Extra tables, mostly used by indicators --- Extra tables, mostly used by indicators
create table ${stats_db_name}.result_projectcount as create table ${stats_db_name}.result_projectcount STORED AS PARQUET as
select r.id, count(distinct p.id) as count select r.id, count(distinct p.id) as count
from ${stats_db_name}.result r from ${stats_db_name}.result r
left outer join ${stats_db_name}.result_projects rp on rp.id=r.id left outer join ${stats_db_name}.result_projects rp on rp.id=r.id
left outer join ${stats_db_name}.project p on p.id=rp.project left outer join ${stats_db_name}.project p on p.id=rp.project
group by r.id; group by r.id;
create table ${stats_db_name}.result_fundercount as create table ${stats_db_name}.result_fundercount STORED AS PARQUET as
select r.id, count(distinct p.funder) as count select r.id, count(distinct p.funder) as count
from ${stats_db_name}.result r from ${stats_db_name}.result r
left outer join ${stats_db_name}.result_projects rp on rp.id=r.id left outer join ${stats_db_name}.result_projects rp on rp.id=r.id
left outer join ${stats_db_name}.project p on p.id=rp.project left outer join ${stats_db_name}.project p on p.id=rp.project
group by r.id; group by r.id;
create table ${stats_db_name}.project_resultcount as create table ${stats_db_name}.project_resultcount STORED AS PARQUET as
with rcount as ( with rcount as (
select p.id as pid, count(distinct r.id) as `count`, r.type as type select p.id as pid, count(distinct r.id) as `count`, r.type as type
from ${stats_db_name}.project p from ${stats_db_name}.project p

6
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql
View File

@ -265,19 +265,19 @@ left outer join (
create table indi_org_openess stored as parquet as create table indi_org_openess stored as parquet as
WITH datasets_oa as ( WITH datasets_oa as (
SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa_new dg SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa dg
join openaire_prod_stats.result_organization ro on dg.id=ro.id join openaire_prod_stats.result_organization ro on dg.id=ro.id
join openaire_prod_stats.dataset ds on dg.id=ds.id join openaire_prod_stats.dataset ds on dg.id=ds.id
WHERE dg.is_gold=1 WHERE dg.is_gold=1
group by ro.organization), group by ro.organization),
software_oa as ( software_oa as (
SELECT ro.organization, count(dg.id) no_oasoftware FROM indi_software_gold_oa_new dg SELECT ro.organization, count(dg.id) no_oasoftware FROM indi_software_gold_oa dg
join openaire_prod_stats.result_organization ro on dg.id=ro.id join openaire_prod_stats.result_organization ro on dg.id=ro.id
join openaire_prod_stats.software ds on dg.id=ds.id join openaire_prod_stats.software ds on dg.id=ds.id
WHERE dg.is_gold=1 WHERE dg.is_gold=1
group by ro.organization), group by ro.organization),
pubs_oa as ( pubs_oa as (
SELECT ro.organization, count(dg.id) no_oapubs FROM indi_pub_gold_oa_new dg SELECT ro.organization, count(dg.id) no_oapubs FROM indi_pub_gold_oa dg
join openaire_prod_stats.result_organization ro on dg.id=ro.id join openaire_prod_stats.result_organization ro on dg.id=ro.id
join openaire_prod_stats.publication ds on dg.id=ds.id join openaire_prod_stats.publication ds on dg.id=ds.id
where dg.is_gold=1 where dg.is_gold=1

6
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql
View File

@ -3,20 +3,20 @@
---------------------------------------------------- ----------------------------------------------------
-- Peer reviewed: -- Peer reviewed:
create table ${stats_db_name}.result_peerreviewed as create table ${stats_db_name}.result_peerreviewed STORED AS PARQUET as
select r.id as id, case when doi.doi_from_crossref=1 and grey.grey_lit=0 then true else false end as peer_reviewed select r.id as id, case when doi.doi_from_crossref=1 and grey.grey_lit=0 then true else false end as peer_reviewed
from ${stats_db_name}.result r from ${stats_db_name}.result r
left outer join ${stats_db_name}.indi_pub_doi_from_crossref doi on doi.id=r.id left outer join ${stats_db_name}.indi_pub_doi_from_crossref doi on doi.id=r.id
left outer join ${stats_db_name}.indi_pub_grey_lit grey on grey.id=r.id; left outer join ${stats_db_name}.indi_pub_grey_lit grey on grey.id=r.id;
-- Green OA: -- Green OA:
create table ${stats_db_name}.result_greenoa as create table ${stats_db_name}.result_greenoa STORED AS PARQUET as
select r.id, case when green.green_oa=1 then true else false end as green select r.id, case when green.green_oa=1 then true else false end as green
from ${stats_db_name}.result r from ${stats_db_name}.result r
left outer join ${stats_db_name}.indi_pub_green_oa green on green.id=r.id; left outer join ${stats_db_name}.indi_pub_green_oa green on green.id=r.id;
-- GOLD OA: -- GOLD OA:
create table ${stats_db_name}.result_gold as create table ${stats_db_name}.result_gold STORED AS PARQUET as
select r.id, case when gold.is_gold=1 then true else false end as gold select r.id, case when gold.is_gold=1 then true else false end as gold
from ${stats_db_name}.result r from ${stats_db_name}.result r
left outer join ${stats_db_name}.indi_pub_gold_oa gold on gold.id=r.id; left outer join ${stats_db_name}.indi_pub_gold_oa gold on gold.id=r.id;

16
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
View File

@ -40,13 +40,13 @@ SELECT substr(p.id, 4) as id,
from ${openaire_db_name}.publication p from ${openaire_db_name}.publication p
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.publication_classifications AS CREATE TABLE ${stats_db_name}.publication_classifications STORED AS PARQUET AS
SELECT substr(p.id, 4) as id, instancetype.classname as type SELECT substr(p.id, 4) as id, instancetype.classname as type
from ${openaire_db_name}.publication p from ${openaire_db_name}.publication p
LATERAL VIEW explode(p.instance.instancetype) instances as instancetype LATERAL VIEW explode(p.instance.instancetype) instances as instancetype
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.publication_concepts AS CREATE TABLE ${stats_db_name}.publication_concepts STORED AS PARQUET AS
SELECT substr(p.id, 4) as id, case SELECT substr(p.id, 4) as id, case
when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other') when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other')
@ -55,7 +55,7 @@ from ${openaire_db_name}.publication p
LATERAL VIEW explode(p.context) contexts as context LATERAL VIEW explode(p.context) contexts as context
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.publication_datasources as CREATE TABLE ${stats_db_name}.publication_datasources STORED AS PARQUET as
SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource
FROM ( FROM (
SELECT substr(p.id, 4) as id, substr(instances.instance.hostedby.key, 4) as datasource SELECT substr(p.id, 4) as id, substr(instances.instance.hostedby.key, 4) as datasource
@ -66,30 +66,30 @@ FROM (
from ${openaire_db_name}.datasource d from ${openaire_db_name}.datasource d
WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id; WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id;
CREATE TABLE ${stats_db_name}.publication_languages AS CREATE TABLE ${stats_db_name}.publication_languages STORED AS PARQUET AS
select substr(p.id, 4) as id, p.language.classname as language select substr(p.id, 4) as id, p.language.classname as language
FROM ${openaire_db_name}.publication p FROM ${openaire_db_name}.publication p
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.publication_oids AS CREATE TABLE ${stats_db_name}.publication_oids STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, oids.ids AS oid SELECT substr(p.id, 4) AS id, oids.ids AS oid
FROM ${openaire_db_name}.publication p FROM ${openaire_db_name}.publication p
LATERAL VIEW explode(p.originalid) oids AS ids LATERAL VIEW explode(p.originalid) oids AS ids
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.publication_pids AS CREATE TABLE ${stats_db_name}.publication_pids STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value as pid SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value as pid
FROM ${openaire_db_name}.publication p FROM ${openaire_db_name}.publication p
LATERAL VIEW explode(p.pid) pids AS ppid LATERAL VIEW explode(p.pid) pids AS ppid
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.publication_topics as CREATE TABLE ${stats_db_name}.publication_topics STORED AS PARQUET as
select substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS TYPE, subjects.subject.value AS topic select substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS TYPE, subjects.subject.value AS topic
FROM ${openaire_db_name}.publication p FROM ${openaire_db_name}.publication p
LATERAL VIEW explode(p.subject) subjects AS subject LATERAL VIEW explode(p.subject) subjects AS subject
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.publication_citations AS CREATE TABLE ${stats_db_name}.publication_citations STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
FROM ${openaire_db_name}.publication p FROM ${openaire_db_name}.publication p
lateral view explode(p.extrainfo) citations AS citation lateral view explode(p.extrainfo) citations AS citation

28
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql
View File

@ -22,7 +22,16 @@ create table TARGET.result stored as parquet as
'openorgs____::b84450f9864182c67b8611b5593f4250', 'openorgs____::b84450f9864182c67b8611b5593f4250',
'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', 'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975',
'openorgs____::eadc8da90a546e98c03f896661a2e4d4', 'openorgs____::eadc8da90a546e98c03f896661a2e4d4',
'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2') )) foo; 'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2',
'openorgs____::d169c7407dd417152596908d48c11460',
'openorgs____::1ec924b1759bb16d0a02f2dad8689b21',
'openorgs____::2fb1e47b4612688d9de9169d579939a7',
'openorgs____::759d59f05d77188faee99b7493b46805',
'openorgs____::cad284878801b9465fa51a95b1d779db',
'openorgs____::eadc8da90a546e98c03f896661a2e4d4',
'openorgs____::c0286313e36479eff8676dba9b724b40'
-- ,'openorgs____::c80a8243a5e5c620d7931c88d93bf17a' -- Paris Diderot
) )) foo;
compute stats TARGET.result; compute stats TARGET.result;
create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id);
@ -52,7 +61,7 @@ compute stats TARGET.result_languages;
create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_licenses; compute stats TARGET.result_licenses;
create table TARGET.licenses_normalized as select * from SOURCE.licenses_normalized; create table TARGET.licenses_normalized STORED AS PARQUET as select * from SOURCE.licenses_normalized;
create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id); create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_oids; compute stats TARGET.result_oids;
@ -81,9 +90,14 @@ compute stats TARGET.result_sources;
create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_topics; compute stats TARGET.result_topics;
create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_apc;
create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result); create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result);
create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result); create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result);
create table TARGET.result_result as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou;
drop view TARGET.foo1; drop view TARGET.foo1;
drop view TARGET.foo2; drop view TARGET.foo2;
compute stats TARGET.result_result; compute stats TARGET.result_result;
@ -157,13 +171,13 @@ create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess;
create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id); create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.indi_pub_hybrid_oa_with_cc; compute stats TARGET.indi_pub_hybrid_oa_with_cc;
create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.id); create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
compute stats TARGET.indi_pub_downloads; compute stats TARGET.indi_pub_downloads;
create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.id); create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
compute stats TARGET.indi_pub_downloads_datasource; compute stats TARGET.indi_pub_downloads_datasource;
create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.id); create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
compute stats TARGET.indi_pub_downloads_year; compute stats TARGET.indi_pub_downloads_year;
create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.id); create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);
compute stats TARGET.indi_pub_downloads_datasource_year; compute stats TARGET.indi_pub_downloads_datasource_year;
--denorm --denorm

16
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
View File

@ -40,20 +40,20 @@ SELECT substr(d.id, 4) AS id,
FROM ${openaire_db_name}.dataset d FROM ${openaire_db_name}.dataset d
WHERE d.datainfo.deletedbyinference = FALSE and d.datainfo.invisible=false; WHERE d.datainfo.deletedbyinference = FALSE and d.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.dataset_citations AS CREATE TABLE ${stats_db_name}.dataset_citations STORED AS PARQUET AS
SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
FROM ${openaire_db_name}.dataset d FROM ${openaire_db_name}.dataset d
LATERAL VIEW explode(d.extrainfo) citations AS citation LATERAL VIEW explode(d.extrainfo) citations AS citation
WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
and d.datainfo.deletedbyinference = false and d.datainfo.invisible=false; and d.datainfo.deletedbyinference = false and d.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.dataset_classifications AS CREATE TABLE ${stats_db_name}.dataset_classifications STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, instancetype.classname AS type SELECT substr(p.id, 4) AS id, instancetype.classname AS type
FROM ${openaire_db_name}.dataset p FROM ${openaire_db_name}.dataset p
LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.dataset_concepts AS CREATE TABLE ${stats_db_name}.dataset_concepts STORED AS PARQUET AS
SELECT substr(p.id, 4) as id, case SELECT substr(p.id, 4) as id, case
when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other') when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other')
@ -62,7 +62,7 @@ from ${openaire_db_name}.dataset p
LATERAL VIEW explode(p.context) contexts as context LATERAL VIEW explode(p.context) contexts as context
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.dataset_datasources AS CREATE TABLE ${stats_db_name}.dataset_datasources STORED AS PARQUET AS
SELECT p.id, case when d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource SELECT p.id, case when d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource
FROM ( FROM (
SELECT substr(p.id, 4) as id, substr(instances.instance.hostedby.key, 4) AS datasource SELECT substr(p.id, 4) as id, substr(instances.instance.hostedby.key, 4) AS datasource
@ -74,24 +74,24 @@ FROM (
FROM ${openaire_db_name}.datasource d FROM ${openaire_db_name}.datasource d
WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d ON p.datasource = d.id; WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d ON p.datasource = d.id;
CREATE TABLE ${stats_db_name}.dataset_languages AS CREATE TABLE ${stats_db_name}.dataset_languages STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, p.language.classname AS language SELECT substr(p.id, 4) AS id, p.language.classname AS language
FROM ${openaire_db_name}.dataset p FROM ${openaire_db_name}.dataset p
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.dataset_oids AS CREATE TABLE ${stats_db_name}.dataset_oids STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, oids.ids AS oid SELECT substr(p.id, 4) AS id, oids.ids AS oid
FROM ${openaire_db_name}.dataset p FROM ${openaire_db_name}.dataset p
LATERAL VIEW explode(p.originalid) oids AS ids LATERAL VIEW explode(p.originalid) oids AS ids
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.dataset_pids AS CREATE TABLE ${stats_db_name}.dataset_pids STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid
FROM ${openaire_db_name}.dataset p FROM ${openaire_db_name}.dataset p
LATERAL VIEW explode(p.pid) pids AS ppid LATERAL VIEW explode(p.pid) pids AS ppid
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.dataset_topics AS CREATE TABLE ${stats_db_name}.dataset_topics STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic
FROM ${openaire_db_name}.dataset p FROM ${openaire_db_name}.dataset p
LATERAL VIEW explode(p.subject) subjects AS subject LATERAL VIEW explode(p.subject) subjects AS subject

16
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
View File

@ -40,20 +40,20 @@ SELECT substr(s.id, 4) as id,
from ${openaire_db_name}.software s from ${openaire_db_name}.software s
where s.datainfo.deletedbyinference = false and s.datainfo.invisible=false; where s.datainfo.deletedbyinference = false and s.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.software_citations AS CREATE TABLE ${stats_db_name}.software_citations STORED AS PARQUET AS
SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
FROM ${openaire_db_name}.software s FROM ${openaire_db_name}.software s
LATERAL VIEW explode(s.extrainfo) citations as citation LATERAL VIEW explode(s.extrainfo) citations as citation
where xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" where xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
and s.datainfo.deletedbyinference = false and s.datainfo.invisible=false; and s.datainfo.deletedbyinference = false and s.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.software_classifications AS CREATE TABLE ${stats_db_name}.software_classifications STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, instancetype.classname AS type SELECT substr(p.id, 4) AS id, instancetype.classname AS type
FROM ${openaire_db_name}.software p FROM ${openaire_db_name}.software p
LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.software_concepts AS CREATE TABLE ${stats_db_name}.software_concepts STORED AS PARQUET AS
SELECT substr(p.id, 4) as id, case SELECT substr(p.id, 4) as id, case
when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other') when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other')
@ -62,7 +62,7 @@ FROM ${openaire_db_name}.software p
LATERAL VIEW explode(p.context) contexts AS context LATERAL VIEW explode(p.context) contexts AS context
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.software_datasources AS CREATE TABLE ${stats_db_name}.software_datasources STORED AS PARQUET AS
SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource end as datasource SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource end as datasource
FROM ( FROM (
SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource
@ -74,24 +74,24 @@ FROM (
FROM ${openaire_db_name}.datasource d FROM ${openaire_db_name}.datasource d
WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d ON p.datasource = d.id; WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d ON p.datasource = d.id;
CREATE TABLE ${stats_db_name}.software_languages AS CREATE TABLE ${stats_db_name}.software_languages STORED AS PARQUET AS
select substr(p.id, 4) AS id, p.language.classname AS language select substr(p.id, 4) AS id, p.language.classname AS language
FROM ${openaire_db_name}.software p FROM ${openaire_db_name}.software p
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.software_oids AS CREATE TABLE ${stats_db_name}.software_oids STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, oids.ids AS oid SELECT substr(p.id, 4) AS id, oids.ids AS oid
FROM ${openaire_db_name}.software p FROM ${openaire_db_name}.software p
LATERAL VIEW explode(p.originalid) oids AS ids LATERAL VIEW explode(p.originalid) oids AS ids
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.software_pids AS CREATE TABLE ${stats_db_name}.software_pids STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid
FROM ${openaire_db_name}.software p FROM ${openaire_db_name}.software p
LATERAL VIEW explode(p.pid) pids AS ppid LATERAL VIEW explode(p.pid) pids AS ppid
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.software_topics AS CREATE TABLE ${stats_db_name}.software_topics STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic
FROM ${openaire_db_name}.software p FROM ${openaire_db_name}.software p
LATERAL VIEW explode(p.subject) subjects AS subject LATERAL VIEW explode(p.subject) subjects AS subject

16
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
View File

@ -40,18 +40,18 @@ FROM ${openaire_db_name}.otherresearchproduct o
WHERE o.datainfo.deletedbyinference = FALSE and o.datainfo.invisible=false; WHERE o.datainfo.deletedbyinference = FALSE and o.datainfo.invisible=false;
-- Otherresearchproduct_citations -- Otherresearchproduct_citations
CREATE TABLE ${stats_db_name}.otherresearchproduct_citations AS CREATE TABLE ${stats_db_name}.otherresearchproduct_citations STORED AS PARQUET AS
SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
FROM ${openaire_db_name}.otherresearchproduct o LATERAL VIEW explode(o.extrainfo) citations AS citation FROM ${openaire_db_name}.otherresearchproduct o LATERAL VIEW explode(o.extrainfo) citations AS citation
WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != "" WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
and o.datainfo.deletedbyinference = false and o.datainfo.invisible=false; and o.datainfo.deletedbyinference = false and o.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.otherresearchproduct_classifications AS CREATE TABLE ${stats_db_name}.otherresearchproduct_classifications STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, instancetype.classname AS type SELECT substr(p.id, 4) AS id, instancetype.classname AS type
FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.otherresearchproduct_concepts AS CREATE TABLE ${stats_db_name}.otherresearchproduct_concepts STORED AS PARQUET AS
SELECT substr(p.id, 4) as id, case SELECT substr(p.id, 4) as id, case
when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other') when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other')
@ -59,7 +59,7 @@ SELECT substr(p.id, 4) as id, case
FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.context) contexts AS context FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.context) contexts AS context
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.otherresearchproduct_datasources AS CREATE TABLE ${stats_db_name}.otherresearchproduct_datasources STORED AS PARQUET AS
SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource
FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource
from ${openaire_db_name}.otherresearchproduct p lateral view explode(p.instance) instances as instance from ${openaire_db_name}.otherresearchproduct p lateral view explode(p.instance) instances as instance
@ -68,22 +68,22 @@ FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) A
from ${openaire_db_name}.datasource d from ${openaire_db_name}.datasource d
WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id; WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id;
CREATE TABLE ${stats_db_name}.otherresearchproduct_languages AS CREATE TABLE ${stats_db_name}.otherresearchproduct_languages STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, p.language.classname AS language SELECT substr(p.id, 4) AS id, p.language.classname AS language
FROM ${openaire_db_name}.otherresearchproduct p FROM ${openaire_db_name}.otherresearchproduct p
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.otherresearchproduct_oids AS CREATE TABLE ${stats_db_name}.otherresearchproduct_oids STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, oids.ids AS oid SELECT substr(p.id, 4) AS id, oids.ids AS oid
FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.originalid) oids AS ids FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.originalid) oids AS ids
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.otherresearchproduct_pids AS CREATE TABLE ${stats_db_name}.otherresearchproduct_pids STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid
FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.pid) pids AS ppid FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.pid) pids AS ppid
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.otherresearchproduct_topics AS CREATE TABLE ${stats_db_name}.otherresearchproduct_topics STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic
FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject
where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;

10
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql
View File

@ -3,24 +3,24 @@
-- Project table/view and Project related tables/views -- Project table/view and Project related tables/views
------------------------------------------------------ ------------------------------------------------------
------------------------------------------------------ ------------------------------------------------------
CREATE TABLE ${stats_db_name}.project_oids AS CREATE TABLE ${stats_db_name}.project_oids STORED AS PARQUET AS
SELECT substr(p.id, 4) AS id, oids.ids AS oid SELECT substr(p.id, 4) AS id, oids.ids AS oid
FROM ${openaire_db_name}.project p LATERAL VIEW explode(p.originalid) oids AS ids FROM ${openaire_db_name}.project p LATERAL VIEW explode(p.originalid) oids AS ids
where p.datainfo.deletedbyinference=false and p.datainfo.invisible=false; where p.datainfo.deletedbyinference=false and p.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.project_organizations AS CREATE TABLE ${stats_db_name}.project_organizations STORED AS PARQUET AS
SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization
from ${openaire_db_name}.relation r from ${openaire_db_name}.relation r
WHERE r.reltype = 'projectOrganization' WHERE r.reltype = 'projectOrganization'
and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.project_results AS CREATE TABLE ${stats_db_name}.project_results STORED AS PARQUET AS
SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result, r.datainfo.provenanceaction.classname as provenance SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result, r.datainfo.provenanceaction.classname as provenance
FROM ${openaire_db_name}.relation r FROM ${openaire_db_name}.relation r
WHERE r.reltype = 'resultProject' WHERE r.reltype = 'resultProject'
and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false;
create table ${stats_db_name}.project_classification as create table ${stats_db_name}.project_classification STORED AS PARQUET as
select substr(p.id, 4) as id, class.h2020programme.code, class.level1, class.level2, class.level3 select substr(p.id, 4) as id, class.h2020programme.code, class.level1, class.level2, class.level3
from ${openaire_db_name}.project p from ${openaire_db_name}.project p
lateral view explode(p.h2020classification) classifs as class lateral view explode(p.h2020classification) classifs as class
@ -76,7 +76,7 @@ SELECT substr(p.id, 4) AS id,
FROM ${openaire_db_name}.project p FROM ${openaire_db_name}.project p
WHERE p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; WHERE p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
create table ${stats_db_name}.funder as create table ${stats_db_name}.funder STORED AS PARQUET as
select distinct xpath_string(fund, '//funder/id') as id, select distinct xpath_string(fund, '//funder/id') as id,
xpath_string(fund, '//funder/name') as name, xpath_string(fund, '//funder/name') as name,
xpath_string(fund, '//funder/shortname') as shortname xpath_string(fund, '//funder/shortname') as shortname

4
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
View File

@ -123,13 +123,13 @@ UNION ALL
SELECT * SELECT *
FROM ${stats_db_name}.otherresearchproduct_topics; FROM ${stats_db_name}.otherresearchproduct_topics;
CREATE TABLE ${stats_db_name}.result_organization AS CREATE TABLE ${stats_db_name}.result_organization STORED AS PARQUET AS
SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization
FROM ${openaire_db_name}.relation r FROM ${openaire_db_name}.relation r
WHERE r.reltype = 'resultOrganization' WHERE r.reltype = 'resultOrganization'
and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.result_projects AS CREATE TABLE ${stats_db_name}.result_projects STORED AS PARQUET AS
select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend, pr.provenance as provenance select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend, pr.provenance as provenance
FROM ${stats_db_name}.result r FROM ${stats_db_name}.result r
JOIN ${stats_db_name}.project_results pr ON r.id = pr.result JOIN ${stats_db_name}.project_results pr ON r.id = pr.result

8
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
View File

@ -80,24 +80,24 @@ UPDATE ${stats_db_name}.datasource_tmp
SET yearofvalidation=null SET yearofvalidation=null
WHERE yearofvalidation = '-1'; WHERE yearofvalidation = '-1';
CREATE TABLE ${stats_db_name}.datasource_languages AS CREATE TABLE ${stats_db_name}.datasource_languages STORED AS PARQUET AS
SELECT substr(d.id, 4) AS id, langs.languages AS language SELECT substr(d.id, 4) AS id, langs.languages AS language
FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.odlanguages.value) langs AS languages FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.odlanguages.value) langs AS languages
where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.datasource_oids AS CREATE TABLE ${stats_db_name}.datasource_oids STORED AS PARQUET AS
SELECT substr(d.id, 4) AS id, oids.ids AS oid SELECT substr(d.id, 4) AS id, oids.ids AS oid
FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.originalid) oids AS ids FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.originalid) oids AS ids
where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false;
CREATE TABLE ${stats_db_name}.datasource_organizations AS CREATE TABLE ${stats_db_name}.datasource_organizations STORED AS PARQUET AS
SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization
FROM ${openaire_db_name}.relation r FROM ${openaire_db_name}.relation r
WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false;
-- datasource sources: -- datasource sources:
-- where the datasource info have been collected from. -- where the datasource info have been collected from.
create table if not exists ${stats_db_name}.datasource_sources AS create table if not exists ${stats_db_name}.datasource_sources STORED AS PARQUET AS
select substr(d.id, 4) as id, substr(cf.key, 4) as datasource select substr(d.id, 4) as id, substr(cf.key, 4) as datasource
from ${openaire_db_name}.datasource d lateral view explode(d.collectedfrom) cfrom as cf from ${openaire_db_name}.datasource d lateral view explode(d.collectedfrom) cfrom as cf
where d.datainfo.deletedbyinference = false and d.datainfo.invisible=false; where d.datainfo.deletedbyinference = false and d.datainfo.invisible=false;

7
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql
View File

@ -3,7 +3,7 @@
-- Organization table/view and Organization related tables/views -- Organization table/view and Organization related tables/views
---------------------------------------------------------------- ----------------------------------------------------------------
---------------------------------------------------------------- ----------------------------------------------------------------
CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization AS CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization STORED AS PARQUET AS
SELECT substr(o.id, 4) as id, SELECT substr(o.id, 4) as id,
o.legalname.value as name, o.legalname.value as name,
o.legalshortname.value as legalshortname, o.legalshortname.value as legalshortname,
@ -17,7 +17,4 @@ FROM ${stats_db_name}.datasource_organizations;
CREATE OR REPLACE VIEW ${stats_db_name}.organization_projects AS CREATE OR REPLACE VIEW ${stats_db_name}.organization_projects AS
SELECT id AS project, organization as id SELECT id AS project, organization as id
FROM ${stats_db_name}.project_organizations; FROM ${stats_db_name}.project_organizations;
-- ANALYZE TABLE ${stats_db_name}.organization COMPUTE STATISTICS;
-- ANALYZE TABLE ${stats_db_name}.organization COMPUTE STATISTICS FOR COLUMNS;

2
pom.xml
View File

@ -797,7 +797,7 @@
<mockito-core.version>3.3.3</mockito-core.version> <mockito-core.version>3.3.3</mockito-core.version>
<mongodb.driver.version>3.4.2</mongodb.driver.version> <mongodb.driver.version>3.4.2</mongodb.driver.version>
<vtd.version>[2.12,3.0)</vtd.version> <vtd.version>[2.12,3.0)</vtd.version>
<dhp-schemas.version>[2.10.29]</dhp-schemas.version> <dhp-schemas.version>[2.10.32]</dhp-schemas.version>
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version> <dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version> <dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version> <dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>