forked from D-Net/dnet-hadoop
Merge branch 'beta' into 8232-mdstore-synch-improve
This commit is contained in:
commit
cd3a51a15f
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|
@ -8,13 +8,13 @@ import java.io.Serializable;
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|||
import java.util.Arrays;
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import java.util.List;
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||||
import java.util.Optional;
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import eu.dnetlib.dhp.schema.oaf.*;
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||||
import org.apache.commons.io.IOUtils;
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||||
import org.apache.hadoop.io.Text;
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import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.MapGroupsFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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||||
|
|
@ -28,9 +28,6 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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|||
import eu.dnetlib.dhp.common.HdfsSupport;
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||||
import eu.dnetlib.dhp.schema.action.AtomicAction;
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||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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||||
import eu.dnetlib.dhp.schema.oaf.Measure;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import scala.Tuple2;
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@ -76,41 +73,38 @@ public class SparkAtomicActionUsageJob implements Serializable {
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isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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prepareResults(dbname, spark, workingPath);
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prepareData(dbname, spark, workingPath + "/usageDb", "usage_stats", "result_id");
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prepareData(dbname, spark, workingPath + "/projectDb", "project_stats", "id");
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prepareData(dbname, spark, workingPath + "/datasourceDb", "datasource_stats", "repositor_id");
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||||
writeActionSet(spark, workingPath, outputPath);
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});
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}
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public static void prepareResults(String db, SparkSession spark, String workingPath) {
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private static void prepareData(String dbname, SparkSession spark, String workingPath, String tableName, String attribute_name) {
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spark
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.sql(
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||||
"Select result_id, downloads, views " +
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||||
"from " + db + ".usage_stats")
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.as(Encoders.bean(UsageStatsModel.class))
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||||
.write()
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||||
.mode(SaveMode.Overwrite)
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||||
.option("compression", "gzip")
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||||
.json(workingPath);
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||||
.sql(
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"Select " + attribute_name + " as id, sum(downloads) as downloads, sum(views) as views " +
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"from " + dbname + "." + tableName +
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"group by " + attribute_name)
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.as(Encoders.bean(UsageStatsModel.class))
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||||
.write()
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.mode(SaveMode.Overwrite)
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||||
.option("compression", "gzip")
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||||
.json(workingPath);
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}
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public static void writeActionSet(SparkSession spark, String inputPath, String outputPath) {
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readPath(spark, inputPath, UsageStatsModel.class)
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.groupByKey((MapFunction<UsageStatsModel, String>) us -> us.getResult_id(), Encoders.STRING())
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.mapGroups((MapGroupsFunction<String, UsageStatsModel, Result>) (k, it) -> {
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UsageStatsModel first = it.next();
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it.forEachRemaining(us -> {
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first.setDownloads(first.getDownloads() + us.getDownloads());
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first.setViews(first.getViews() + us.getViews());
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});
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Result res = new Result();
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res.setId("50|" + k);
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res.setMeasures(getMeasure(first.getDownloads(), first.getViews()));
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return res;
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}, Encoders.bean(Result.class))
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.toJavaRDD()
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||||
.map(p -> new AtomicAction(p.getClass(), p))
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||||
getFinalIndicatorsResult(spark, inputPath+ "/usageDb").
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||||
toJavaRDD().
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||||
map(p -> new AtomicAction(p.getClass(),p))
|
||||
.union(getFinalIndicatorsProject(spark, inputPath + "/projectDb")
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||||
.toJavaRDD()
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||||
.map(p -> new AtomicAction(p.getClass(), p )))
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||||
.union(getFinalIndicatorsDatasource(spark, inputPath + "/datasourceDb")
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||||
.toJavaRDD()
|
||||
.map(p -> new AtomicAction(p.getClass(), p)))
|
||||
.mapToPair(
|
||||
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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||||
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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||||
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|
@ -118,6 +112,41 @@ public class SparkAtomicActionUsageJob implements Serializable {
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|||
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||||
}
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||||
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||||
private static Dataset<Result> getFinalIndicatorsResult(SparkSession spark, String inputPath) {
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||||
|
||||
return readPath(spark, inputPath, UsageStatsModel.class)
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||||
.map((MapFunction<UsageStatsModel, Result>) usm -> {
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||||
Result r = new Result();
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||||
r.setId("50|" + usm.getId());
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||||
r.setMeasures(getMeasure(usm.getDownloads(), usm.getViews()));
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||||
return r;
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||||
}, Encoders.bean(Result.class));
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||||
}
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||||
|
||||
private static Dataset<Project> getFinalIndicatorsProject(SparkSession spark, String inputPath) {
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||||
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||||
return readPath(spark, inputPath, UsageStatsModel.class)
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||||
.map((MapFunction<UsageStatsModel, Project>) usm -> {
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||||
Project r = new Project();
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||||
r.setId("40|" + usm.getId());
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||||
r.setMeasures(getMeasure(usm.getDownloads(), usm.getViews()));
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||||
return r;
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||||
}, Encoders.bean(Project.class));
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||||
}
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||||
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||||
private static Dataset<Datasource> getFinalIndicatorsDatasource(SparkSession spark, String inputPath) {
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||||
|
||||
return readPath(spark, inputPath, UsageStatsModel.class)
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||||
.map((MapFunction<UsageStatsModel, Datasource>) usm -> {
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||||
Datasource r = new Datasource();
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||||
r.setId("10|" + usm.getId());
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||||
r.setMeasures(getMeasure(usm.getDownloads(), usm.getViews()));
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||||
return r;
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||||
}, Encoders.bean(Datasource.class));
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||||
}
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||||
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||||
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||||
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||||
private static List<Measure> getMeasure(Long downloads, Long views) {
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DataInfo dataInfo = OafMapperUtils
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.dataInfo(
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|
|
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|
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@ -4,16 +4,16 @@ package eu.dnetlib.dhp.actionmanager.usagestats;
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|||
import java.io.Serializable;
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||||
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||||
public class UsageStatsModel implements Serializable {
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||||
private String result_id;
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||||
private String id;
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||||
private Long downloads;
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||||
private Long views;
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||||
|
||||
public String getResult_id() {
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||||
return result_id;
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||||
public String getId() {
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||||
return id;
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||||
}
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||||
|
||||
public void setResult_id(String result_id) {
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||||
this.result_id = result_id;
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||||
public void setId(String id) {
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||||
this.id = id;
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||||
}
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||||
|
||||
public Long getDownloads() {
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||||
|
|
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|||
|
|
@ -89,7 +89,7 @@
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|||
<arg>--hive_metastore_uris</arg><arg>${hiveMetastoreUris}</arg>
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||||
<arg>--outputPath</arg><arg>${outputPath}</arg>
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||||
<arg>--usagestatsdb</arg><arg>${usagestatsdb}</arg>
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||||
<arg>--workingPath</arg><arg>${workingDir}/usageDb</arg>
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||||
<arg>--workingPath</arg><arg>${workingDir}</arg>
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||||
</spark>
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||||
<ok to="End"/>
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||||
<error to="Kill"/>
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||||
|
|
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|||
|
|
@ -8,6 +8,7 @@ import java.nio.file.Files;
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|||
import java.nio.file.Path;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
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||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.hadoop.io.Text;
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||||
import org.apache.spark.SparkConf;
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||||
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|
@ -68,24 +69,26 @@ public class SparkAtomicActionCountJobTest {
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|||
@Test
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||||
void testMatch() {
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||||
String usageScoresPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb")
|
||||
.getResource("/eu/dnetlib/dhp/actionmanager/usagestats")
|
||||
.getPath();
|
||||
|
||||
SparkAtomicActionUsageJob.writeActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet");
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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||||
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||||
JavaRDD<Result> tmp = sc
|
||||
JavaRDD<AtomicAction> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
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||||
.map(usm -> OBJECT_MAPPER.readValue(usm._2.getBytes(), AtomicAction.class))
|
||||
.map(aa -> (Result) aa.getPayload());
|
||||
.map(usm -> OBJECT_MAPPER.readValue(usm._2.getBytes(), AtomicAction.class));
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||||
//.map(aa -> (Result) aa.getPayload());
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||||
|
||||
Assertions.assertEquals(9, tmp.count());
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||||
Assertions.assertEquals(9,tmp.filter(aa -> ((OafEntity) aa.getPayload()).getId().startsWith("50|")).count());
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||||
Assertions.assertEquals(9,tmp.filter(aa -> ((OafEntity) aa.getPayload()).getId().startsWith("10|")).count());
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||||
Assertions.assertEquals(9,tmp.filter(aa -> ((OafEntity) aa.getPayload()).getId().startsWith("40|")).count());
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||||
|
||||
tmp.foreach(r -> Assertions.assertEquals(2, r.getMeasures().size()));
|
||||
tmp.foreach(r -> Assertions.assertEquals(2, ((OafEntity)r.getPayload()).getMeasures().size()));
|
||||
tmp
|
||||
.foreach(
|
||||
r -> r
|
||||
r -> ((OafEntity)r.getPayload())
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.forEach(
|
||||
|
|
@ -95,14 +98,14 @@ public class SparkAtomicActionCountJobTest {
|
|||
.forEach(u -> Assertions.assertFalse(u.getDataInfo().getDeletedbyinference()))));
|
||||
tmp
|
||||
.foreach(
|
||||
r -> r
|
||||
r -> ((OafEntity)r.getPayload())
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.forEach(
|
||||
m -> m.getUnit().stream().forEach(u -> Assertions.assertTrue(u.getDataInfo().getInferred()))));
|
||||
tmp
|
||||
.foreach(
|
||||
r -> r
|
||||
r -> ((OafEntity)r.getPayload())
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.forEach(
|
||||
|
|
@ -113,7 +116,7 @@ public class SparkAtomicActionCountJobTest {
|
|||
|
||||
tmp
|
||||
.foreach(
|
||||
r -> r
|
||||
r -> ((OafEntity)r.getPayload())
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.forEach(
|
||||
|
|
@ -127,7 +130,7 @@ public class SparkAtomicActionCountJobTest {
|
|||
u.getDataInfo().getProvenanceaction().getClassid()))));
|
||||
tmp
|
||||
.foreach(
|
||||
r -> r
|
||||
r -> ((OafEntity)r.getPayload())
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.forEach(
|
||||
|
|
@ -142,7 +145,7 @@ public class SparkAtomicActionCountJobTest {
|
|||
|
||||
tmp
|
||||
.foreach(
|
||||
r -> r
|
||||
r -> ((OafEntity)r.getPayload())
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.forEach(
|
||||
|
|
@ -157,12 +160,13 @@ public class SparkAtomicActionCountJobTest {
|
|||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1, tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).count());
|
||||
1, tmp.filter(r -> ((OafEntity)r.getPayload()).getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"0",
|
||||
tmp
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6"))
|
||||
.collect()
|
||||
.get(0)
|
||||
|
|
@ -178,7 +182,8 @@ public class SparkAtomicActionCountJobTest {
|
|||
.assertEquals(
|
||||
"5",
|
||||
tmp
|
||||
.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6"))
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
|
|
@ -194,7 +199,8 @@ public class SparkAtomicActionCountJobTest {
|
|||
.assertEquals(
|
||||
"0",
|
||||
tmp
|
||||
.filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0"))
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
|
|
@ -209,7 +215,8 @@ public class SparkAtomicActionCountJobTest {
|
|||
.assertEquals(
|
||||
"1",
|
||||
tmp
|
||||
.filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0"))
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
|
|
@ -225,7 +232,8 @@ public class SparkAtomicActionCountJobTest {
|
|||
.assertEquals(
|
||||
"2",
|
||||
tmp
|
||||
.filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f"))
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
|
|
@ -240,7 +248,8 @@ public class SparkAtomicActionCountJobTest {
|
|||
.assertEquals(
|
||||
"6",
|
||||
tmp
|
||||
.filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f"))
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
|
|
@ -251,6 +260,206 @@ public class SparkAtomicActionCountJobTest {
|
|||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"0",
|
||||
tmp
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("40|f1__________::53575dc69e9ace947e02d47ecd54a7a6"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(m -> m.getId().equals("downloads"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"5",
|
||||
tmp
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("40|f1__________::53575dc69e9ace947e02d47ecd54a7a6"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(m -> m.getId().equals("views"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"0",
|
||||
tmp
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("40|f11_________::17eda2ff77407538fbe5d3d719b9d1c0"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(m -> m.getId().equals("downloads"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"1",
|
||||
tmp
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("40|f11_________::17eda2ff77407538fbe5d3d719b9d1c0"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(m -> m.getId().equals("views"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"2",
|
||||
tmp
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("40|f12_________::3085e4c6e051378ca6157fe7f0430c1f"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(m -> m.getId().equals("downloads"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"6",
|
||||
tmp
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("40|f12_________::3085e4c6e051378ca6157fe7f0430c1f"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(m -> m.getId().equals("views"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"0",
|
||||
tmp
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("10|d1__________::53575dc69e9ace947e02d47ecd54a7a6"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(m -> m.getId().equals("downloads"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"5",
|
||||
tmp
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("10|d1__________::53575dc69e9ace947e02d47ecd54a7a6"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(m -> m.getId().equals("views"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"0",
|
||||
tmp
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("10|d11_________::17eda2ff77407538fbe5d3d719b9d1c0"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(m -> m.getId().equals("downloads"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"1",
|
||||
tmp
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("10|d11_________::17eda2ff77407538fbe5d3d719b9d1c0"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(m -> m.getId().equals("views"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"2",
|
||||
tmp
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("10|d12_________::3085e4c6e051378ca6157fe7f0430c1f"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(m -> m.getId().equals("downloads"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"6",
|
||||
tmp
|
||||
.map(r -> ((OafEntity)r.getPayload()))
|
||||
.filter(r -> r.getId().equals("10|d12_________::3085e4c6e051378ca6157fe7f0430c1f"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(m -> m.getId().equals("views"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,9 @@
|
|||
{"id":"d1__________::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":5}
|
||||
{"id":"d11_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1}
|
||||
{"id":"d11_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3}
|
||||
{"id":"d11_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1}
|
||||
{"id":"d12_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":6}
|
||||
{"id":"d12_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1}
|
||||
{"id":"d12_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3}
|
||||
{"id":"d13_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":10}
|
||||
{"id":"d13_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3}
|
||||
|
|
@ -0,0 +1,12 @@
|
|||
{"id":"d1__________::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":4}
|
||||
{"id":"d1__________::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":1}
|
||||
{"id":"d11_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1}
|
||||
{"id":"d11_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3}
|
||||
{"id":"d11_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1}
|
||||
{"id":"d12_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":3}
|
||||
{"id":"d12_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":0,"views":3}
|
||||
{"id":"d12_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1}
|
||||
{"id":"d12_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3}
|
||||
{"id":"d13_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":8}
|
||||
{"id":"d13_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":0,"views":2}
|
||||
{"id":"d13_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3}
|
||||
|
|
@ -0,0 +1,9 @@
|
|||
{"id":"f1__________::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":5}
|
||||
{"id":"f11_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1}
|
||||
{"id":"f11_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3}
|
||||
{"id":"f11_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1}
|
||||
{"id":"f12_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":6}
|
||||
{"id":"f12_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1}
|
||||
{"id":"f12_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3}
|
||||
{"id":"f13_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":10}
|
||||
{"id":"f13_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3}
|
||||
|
|
@ -0,0 +1,12 @@
|
|||
{"id":"f1__________::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":4}
|
||||
{"id":"f1__________::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":1}
|
||||
{"id":"f11_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1}
|
||||
{"id":"f11_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3}
|
||||
{"id":"f11_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1}
|
||||
{"id":"f12_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":3}
|
||||
{"id":"f12_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":0,"views":3}
|
||||
{"id":"f12_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1}
|
||||
{"id":"f12_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3}
|
||||
{"id":"f13_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":8}
|
||||
{"id":"f13_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":0,"views":2}
|
||||
{"id":"f13_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3}
|
||||
|
|
@ -0,0 +1,9 @@
|
|||
{"id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":5}
|
||||
{"id":"doi_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1}
|
||||
{"id":"doi_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3}
|
||||
{"id":"doi_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1}
|
||||
{"id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":6}
|
||||
{"id":"doi_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1}
|
||||
{"id":"doi_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3}
|
||||
{"id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":10}
|
||||
{"id":"doi_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3}
|
||||
|
|
@ -0,0 +1,12 @@
|
|||
{"id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":4}
|
||||
{"id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":1}
|
||||
{"id":"doi_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1}
|
||||
{"id":"doi_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3}
|
||||
{"id":"doi_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1}
|
||||
{"id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":3}
|
||||
{"id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":0,"views":3}
|
||||
{"id":"doi_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1}
|
||||
{"id":"doi_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3}
|
||||
{"id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":8}
|
||||
{"id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":0,"views":2}
|
||||
{"id":"doi_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3}
|
||||
|
|
@ -1,12 +0,0 @@
|
|||
{"result_id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":4}
|
||||
{"result_id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":1}
|
||||
{"result_id":"doi_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1}
|
||||
{"result_id":"doi_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3}
|
||||
{"result_id":"doi_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1}
|
||||
{"result_id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":3}
|
||||
{"result_id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":0,"views":3}
|
||||
{"result_id":"doi_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1}
|
||||
{"result_id":"doi_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3}
|
||||
{"result_id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":8}
|
||||
{"result_id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":0,"views":2}
|
||||
{"result_id":"doi_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3}
|
||||
|
|
@ -37,12 +37,24 @@ public class SubscriptionUtils {
|
|||
}
|
||||
|
||||
public static boolean verifyDateRange(final long date, final String min, final String max) {
|
||||
|
||||
long from = 0;
|
||||
long to = Long.MAX_VALUE;
|
||||
|
||||
try {
|
||||
return date >= DateUtils.parseDate(min, "yyyy-MM-dd").getTime()
|
||||
&& date < DateUtils.parseDate(max, "yyyy-MM-dd").getTime() + ONE_DAY;
|
||||
from = min != null ? DateUtils.parseDate(min, "yyyy-MM-dd").getTime() : 0;
|
||||
} catch (final ParseException e) {
|
||||
return false;
|
||||
from = 0;
|
||||
}
|
||||
|
||||
try {
|
||||
to = max != null ? DateUtils.parseDate(max, "yyyy-MM-dd").getTime() + ONE_DAY : Long.MAX_VALUE;
|
||||
} catch (final ParseException e) {
|
||||
to = Long.MAX_VALUE;
|
||||
}
|
||||
|
||||
return date >= from && date < to;
|
||||
|
||||
}
|
||||
|
||||
public static boolean verifyExact(final String s1, final String s2) {
|
||||
|
|
|
|||
|
|
@ -41,6 +41,18 @@ public class SubscriptionUtilsTest {
|
|||
|
||||
assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", "2011-01-01"));
|
||||
assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", "2021-01-01"));
|
||||
|
||||
assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", "NULL"));
|
||||
assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", null));
|
||||
assertTrue(SubscriptionUtils.verifyDateRange(date, "NULL", "2011-01-01"));
|
||||
assertTrue(SubscriptionUtils.verifyDateRange(date, null, "2011-01-01"));
|
||||
assertTrue(SubscriptionUtils.verifyDateRange(date, "NULL", "NULL"));
|
||||
assertTrue(SubscriptionUtils.verifyDateRange(date, null, null));
|
||||
|
||||
assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", null));
|
||||
assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", "NULL"));
|
||||
assertFalse(SubscriptionUtils.verifyDateRange(date, null, "2005-01-01"));
|
||||
assertFalse(SubscriptionUtils.verifyDateRange(date, "NULL", "2005-01-01"));
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
|
|||
|
|
@ -370,10 +370,50 @@ case object Crossref2Oaf {
|
|||
case dataset: Dataset => convertDataset(dataset)
|
||||
}
|
||||
|
||||
val doisReference: List[String] = for {
|
||||
JObject(reference_json) <- json \ "reference"
|
||||
JField("DOI", JString(doi_json)) <- reference_json
|
||||
} yield doi_json
|
||||
|
||||
if (doisReference != null && doisReference.nonEmpty) {
|
||||
val citation_relations: List[Relation] = generateCitationRelations(doisReference, result)
|
||||
resultList = resultList ::: citation_relations
|
||||
}
|
||||
resultList = resultList ::: List(result)
|
||||
resultList
|
||||
}
|
||||
|
||||
private def createCiteRelation(source: Result, targetPid: String, targetPidType: String): List[Relation] = {
|
||||
|
||||
val targetId = IdentifierFactory.idFromPid("50", targetPidType, targetPid, true)
|
||||
|
||||
val from = new Relation
|
||||
from.setSource(source.getId)
|
||||
from.setTarget(targetId)
|
||||
from.setRelType(ModelConstants.RESULT_RESULT)
|
||||
from.setRelClass(ModelConstants.CITES)
|
||||
from.setSubRelType(ModelConstants.CITATION)
|
||||
from.setCollectedfrom(source.getCollectedfrom)
|
||||
from.setDataInfo(source.getDataInfo)
|
||||
from.setLastupdatetimestamp(source.getLastupdatetimestamp)
|
||||
|
||||
val to = new Relation
|
||||
to.setTarget(source.getId)
|
||||
to.setSource(targetId)
|
||||
to.setRelType(ModelConstants.RESULT_RESULT)
|
||||
to.setRelClass(ModelConstants.IS_CITED_BY)
|
||||
to.setSubRelType(ModelConstants.CITATION)
|
||||
to.setCollectedfrom(source.getCollectedfrom)
|
||||
to.setDataInfo(source.getDataInfo)
|
||||
to.setLastupdatetimestamp(source.getLastupdatetimestamp)
|
||||
|
||||
List(from, to)
|
||||
}
|
||||
|
||||
def generateCitationRelations(dois: List[String], result: Result): List[Relation] = {
|
||||
dois.flatMap(d => createCiteRelation(result, d, "doi"))
|
||||
}
|
||||
|
||||
def mappingFunderToRelations(
|
||||
funders: List[mappingFunder],
|
||||
sourceId: String,
|
||||
|
|
@ -446,6 +486,7 @@ case object Crossref2Oaf {
|
|||
case "10.13039/501100000781" =>
|
||||
generateSimpleRelationFromAward(funder, "corda_______", extractECAward)
|
||||
generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward)
|
||||
generateSimpleRelationFromAward(funder, "corda_____he", extractECAward)
|
||||
case "10.13039/100000001" => generateSimpleRelationFromAward(funder, "nsf_________", a => a)
|
||||
case "10.13039/501100001665" => generateSimpleRelationFromAward(funder, "anr_________", a => a)
|
||||
case "10.13039/501100002341" => generateSimpleRelationFromAward(funder, "aka_________", a => a)
|
||||
|
|
@ -487,6 +528,34 @@ case object Crossref2Oaf {
|
|||
val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63")
|
||||
queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
|
||||
queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
|
||||
//ASAP
|
||||
case "10.13039/100018231" => generateSimpleRelationFromAward(funder, "asap________", a => a)
|
||||
//CHIST-ERA
|
||||
case "10.13039/501100001942" =>
|
||||
val targetId = getProjectId("chistera____", "1e5e62235d094afd01cd56e65112fc63")
|
||||
queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
|
||||
queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
|
||||
//HE
|
||||
case "10.13039/100018693" | "10.13039/100018694" | "10.13039/100019188" | "10.13039/100019180" |
|
||||
"10.13039/100018695" | "10.13039/100019185" | "10.13039/100019186" | "10.13039/100019187" =>
|
||||
generateSimpleRelationFromAward(funder, "corda_____he", extractECAward)
|
||||
//FCT
|
||||
case "10.13039/501100001871" =>
|
||||
generateSimpleRelationFromAward(funder, "fct_________", extractECAward)
|
||||
//NHMRC
|
||||
case "10.13039/501100000925" =>
|
||||
generateSimpleRelationFromAward(funder, "mhmrc_______", extractECAward)
|
||||
//NIH
|
||||
case "10.13039/100000002" =>
|
||||
generateSimpleRelationFromAward(funder, "nih_________", extractECAward)
|
||||
//NWO
|
||||
case "10.13039/501100003246" =>
|
||||
generateSimpleRelationFromAward(funder, "nwo_________", extractECAward)
|
||||
//UKRI
|
||||
case "10.13039/100014013" | "10.13039/501100000267" | "10.13039/501100000268" | "10.13039/501100000269" |
|
||||
"10.13039/501100000266" | "10.13039/501100006041" | "10.13039/501100000265" | "10.13039/501100000270" |
|
||||
"10.13039/501100013589" | "10.13039/501100000271" =>
|
||||
generateSimpleRelationFromAward(funder, "nwo_________", extractECAward)
|
||||
|
||||
case _ => logger.debug("no match for " + funder.DOI.get)
|
||||
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -1,9 +1,14 @@
|
|||
package eu.dnetlib.dhp.doiboost.crossref
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf._
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
|
||||
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
|
||||
import org.json4s
|
||||
import org.json4s.JsonAST.{JField, JObject, JString}
|
||||
import org.json4s.{DefaultFormats, JValue}
|
||||
import org.json4s.jackson.JsonMethods
|
||||
import org.junit.jupiter.api.Assertions._
|
||||
import org.junit.jupiter.api.Test
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
|
@ -109,6 +114,47 @@ class CrossrefMappingTest {
|
|||
|
||||
}
|
||||
|
||||
private def parseJson(input: String): JValue = {
|
||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||
lazy val json: json4s.JValue = JsonMethods.parse(input)
|
||||
|
||||
json
|
||||
}
|
||||
|
||||
@Test
|
||||
def testCitationRelations(): Unit = {
|
||||
val json = Source
|
||||
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo.json"))
|
||||
.mkString
|
||||
|
||||
assertNotNull(json)
|
||||
assertFalse(json.isEmpty)
|
||||
|
||||
val result: List[Oaf] = Crossref2Oaf.convert(json)
|
||||
|
||||
assertTrue(result.nonEmpty)
|
||||
|
||||
val j = parseJson(json)
|
||||
|
||||
val doisReference: List[String] = for {
|
||||
JObject(reference_json) <- j \ "reference"
|
||||
JField("DOI", JString(doi_json)) <- reference_json
|
||||
} yield doi_json
|
||||
|
||||
val relationList: List[Relation] = result
|
||||
.filter(s => s.isInstanceOf[Relation])
|
||||
.map(r => r.asInstanceOf[Relation])
|
||||
.filter(r => r.getSubRelType.equalsIgnoreCase(ModelConstants.CITATION))
|
||||
|
||||
assertNotNull(relationList)
|
||||
assertFalse(relationList.isEmpty)
|
||||
|
||||
assertEquals(doisReference.size * 2, relationList.size)
|
||||
|
||||
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
|
||||
relationList.foreach(p => println(mapper.writeValueAsString(p)))
|
||||
}
|
||||
|
||||
@Test
|
||||
def testEmptyTitle(): Unit = {
|
||||
val json = Source
|
||||
|
|
|
|||
|
|
@ -0,0 +1,32 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
|
||||
<parent>
|
||||
<artifactId>dhp-workflows</artifactId>
|
||||
<groupId>eu.dnetlib.dhp</groupId>
|
||||
<version>1.2.4-SNAPSHOT</version>
|
||||
</parent>
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
<artifactId>dhp-monitor-update</artifactId>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>org.apache.spark</groupId>
|
||||
<artifactId>spark-core_2.11</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.spark</groupId>
|
||||
<artifactId>spark-sql_2.11</artifactId>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>pl.project13.maven</groupId>
|
||||
<artifactId>git-commit-id-plugin</artifactId>
|
||||
<version>2.1.11</version>
|
||||
<configuration>
|
||||
<failOnNoGitDirectory>false</failOnNoGitDirectory>
|
||||
</configuration>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</project>
|
||||
|
|
@ -0,0 +1,34 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>${jobTracker}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>${nameNode}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_jdbc_url</name>
|
||||
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1;?spark.executor.memory=19166291558;spark.yarn.executor.memoryOverhead=3225;spark.driver.memory=11596411699;spark.yarn.driver.memoryOverhead=1228</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.wf.workflow.notification.url</name>
|
||||
<value>{serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>stats_tool_api_url</name>
|
||||
<value>${stats_tool_api_url}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -0,0 +1,18 @@
|
|||
export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs
|
||||
export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami)
|
||||
if ! [ -L $link_folder ]
|
||||
then
|
||||
rm -Rf "$link_folder"
|
||||
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
|
||||
fi
|
||||
|
||||
export SOURCE=$1
|
||||
export TARGET=$2
|
||||
export SCRIPT_PATH=$3
|
||||
|
||||
echo "Getting file from " $3
|
||||
hdfs dfs -copyToLocal $3
|
||||
|
||||
echo "Updating monitor database"
|
||||
cat createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala-shell -f -
|
||||
echo "Impala shell finished"
|
||||
|
|
@ -0,0 +1,146 @@
|
|||
DROP TABLE IF EXISTS TARGET.result_new;
|
||||
|
||||
create table TARGET.result_new as
|
||||
select distinct * from (
|
||||
select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in (
|
||||
-- 'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork
|
||||
-- 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University
|
||||
'openorgs____::57784c9e047e826fefdb1ef816120d92' --Arts et Métiers ParisTech
|
||||
) )) foo;
|
||||
|
||||
COMPUTE STATS TARGET.result_new;
|
||||
|
||||
INSERT INTO TARGET.result select * from TARGET.result_new;
|
||||
COMPUTE STATS TARGET.result;
|
||||
|
||||
INSERT INTO TARGET.result_citations select * from TARGET.result_citations orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_citations;
|
||||
|
||||
INSERT INTO TARGET.result_references_oc select * from TARGET.result_references_oc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_references_oc;
|
||||
|
||||
INSERT INTO TARGET.result_citations_oc select * from TARGET.result_citations_oc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_citations_oc;
|
||||
|
||||
INSERT INTO TARGET.result_classifications select * from TARGET.result_classifications orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_classifications;
|
||||
|
||||
INSERT INTO TARGET.result_apc select * from TARGET.result_apc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_apc;
|
||||
|
||||
INSERT INTO TARGET.result_concepts select * from TARGET.result_concepts orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_concepts;
|
||||
|
||||
INSERT INTO TARGET.result_datasources select * from TARGET.result_datasources orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_datasources;
|
||||
|
||||
INSERT INTO TARGET.result_fundercount select * from TARGET.result_fundercount orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_fundercount;
|
||||
|
||||
INSERT INTO TARGET.result_gold select * from TARGET.result_gold orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_gold;
|
||||
|
||||
INSERT INTO TARGET.result_greenoa select * from TARGET.result_greenoa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_greenoa;
|
||||
|
||||
INSERT INTO TARGET.result_languages select * from TARGET.result_languages orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_languages;
|
||||
|
||||
INSERT INTO TARGET.result_licenses select * from TARGET.result_licenses orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_licenses;
|
||||
|
||||
INSERT INTO TARGET.result_oids select * from TARGET.result_oids orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_oids;
|
||||
|
||||
INSERT INTO TARGET.result_organization select * from TARGET.result_organization orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_organization;
|
||||
|
||||
INSERT INTO TARGET.result_peerreviewed select * from TARGET.result_peerreviewed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_peerreviewed;
|
||||
|
||||
INSERT INTO TARGET.result_pids select * from TARGET.result_pids orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_pids;
|
||||
|
||||
INSERT INTO TARGET.result_projectcount select * from TARGET.result_projectcount orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_projectcount;
|
||||
|
||||
INSERT INTO TARGET.result_projects select * from TARGET.result_projects orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_projects;
|
||||
|
||||
INSERT INTO TARGET.result_refereed select * from TARGET.result_refereed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_refereed;
|
||||
|
||||
INSERT INTO TARGET.result_sources select * from TARGET.result_sources orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_sources;
|
||||
|
||||
INSERT INTO TARGET.result_topics select * from TARGET.result_topics orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_topics;
|
||||
|
||||
INSERT INTO TARGET.result_fos select * from TARGET.result_fos orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.result_fos;
|
||||
|
||||
create view TARGET.foo1 as select * from TARGET.result_result rr where rr.source in (select id from TARGET.result_new);
|
||||
create view TARGET.foo2 as select * from TARGET.result_result rr where rr.target in (select id from TARGET.result_new);
|
||||
INSERT INTO TARGET.result_result select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou;
|
||||
drop view TARGET.foo1;
|
||||
drop view TARGET.foo2;
|
||||
COMPUTE STATS TARGET.result_result;
|
||||
|
||||
-- indicators
|
||||
-- Sprint 1 ----
|
||||
INSERT INTO TARGET.indi_pub_green_oa select * from TARGET.indi_pub_green_oa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_green_oa;
|
||||
INSERT INTO TARGET.indi_pub_grey_lit select * from TARGET.indi_pub_grey_lit orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_grey_lit;
|
||||
INSERT INTO TARGET.indi_pub_doi_from_crossref select * from TARGET.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_doi_from_crossref;
|
||||
-- Sprint 2 ----
|
||||
INSERT INTO TARGET.indi_result_has_cc_licence select * from TARGET.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_result_has_cc_licence;
|
||||
INSERT INTO TARGET.indi_result_has_cc_licence_url select * from TARGET.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_result_has_cc_licence_url;
|
||||
INSERT INTO TARGET.indi_pub_has_abstract select * from TARGET.indi_pub_has_abstract orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_has_abstract;
|
||||
INSERT INTO TARGET.indi_result_with_orcid select * from TARGET.indi_result_with_orcid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_result_with_orcid;
|
||||
---- Sprint 3 ----
|
||||
INSERT INTO TARGET.indi_funded_result_with_fundref select * from TARGET.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_funded_result_with_fundref;
|
||||
---- Sprint 4 ----
|
||||
INSERT INTO TARGET.indi_pub_diamond select * from TARGET.indi_pub_diamond orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_diamond;
|
||||
INSERT INTO TARGET.indi_pub_in_transformative select * from TARGET.indi_pub_in_transformative orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_in_transformative;
|
||||
INSERT INTO TARGET.indi_pub_closed_other_open select * from TARGET.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_closed_other_open;
|
||||
---- Sprint 5 ----
|
||||
INSERT INTO TARGET.indi_result_no_of_copies select * from TARGET.indi_result_no_of_copies orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_result_no_of_copies;
|
||||
---- Sprint 6 ----
|
||||
INSERT INTO TARGET.indi_pub_hybrid_oa_with_cc select * from TARGET.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_hybrid_oa_with_cc;
|
||||
INSERT INTO TARGET.indi_pub_downloads select * from TARGET.indi_pub_downloads orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
|
||||
COMPUTE STATS TARGET.indi_pub_downloads;
|
||||
INSERT INTO TARGET.indi_pub_downloads_datasource select * from TARGET.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
|
||||
COMPUTE STATS TARGET.indi_pub_downloads_datasource;
|
||||
INSERT INTO TARGET.indi_pub_downloads_year select * from TARGET.indi_pub_downloads_year orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
|
||||
COMPUTE STATS TARGET.indi_pub_downloads_year;
|
||||
INSERT INTO TARGET.indi_pub_downloads_datasource_year select * from TARGET.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
|
||||
COMPUTE STATS TARGET.indi_pub_downloads_datasource_year;
|
||||
---- Sprint 7 ----
|
||||
INSERT INTO TARGET.indi_pub_gold_oa select * from TARGET.indi_pub_gold_oa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_gold_oa;
|
||||
INSERT INTO TARGET.indi_pub_hybrid select * from TARGET.indi_pub_hybrid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_hybrid;
|
||||
|
||||
INSERT INTO TARGET.indi_pub_has_preprint select * from TARGET.indi_pub_has_preprint orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_has_preprint;
|
||||
INSERT INTO TARGET.indi_pub_in_subscribed select * from TARGET.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_pub_in_subscribed;
|
||||
INSERT INTO TARGET.indi_result_with_pid select * from TARGET.indi_result_with_pid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
|
||||
COMPUTE STATS TARGET.indi_result_with_pid;
|
||||
--create table TARGET.indi_datasets_gold_oa stored as parquet as select * from SOURCE.indi_datasets_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--compute stats TARGET.indi_datasets_gold_oa;
|
||||
--create table TARGET.indi_software_gold_oa stored as parquet as select * from SOURCE.indi_software_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
--compute stats TARGET.indi_software_gold_oa;
|
||||
DROP TABLE TARGET.result_new;
|
||||
|
|
@ -0,0 +1,77 @@
|
|||
<workflow-app name="Monitor DB" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>stats_db_name</name>
|
||||
<description>the target stats database name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>stats_db_shadow_name</name>
|
||||
<description>the name of the shadow schema</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>monitor_db_name</name>
|
||||
<description>the target monitor db name</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>monitor_db_shadow_name</name>
|
||||
<description>the name of the shadow monitor db</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>stats_tool_api_url</name>
|
||||
<description>The url of the API of the stats tool. Is used to trigger the cache update.</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<description>hive server metastore URIs</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_jdbc_url</name>
|
||||
<description>hive server jdbc url</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_timeout</name>
|
||||
<description>the time period, in seconds, after which Hive fails a transaction if a Hive client has not sent a hearbeat. The default value is 300 seconds.</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>context_api_url</name>
|
||||
<description>the base url of the context api (https://services.openaire.eu/openaire)</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>hive.metastore.uris</name>
|
||||
<value>${hive_metastore_uris}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive.txn.timeout</name>
|
||||
<value>${hive_timeout}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="Step1-createMonitorDB"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="Step1-createMonitorDB">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>monitor.sh</exec>
|
||||
<argument>${stats_db_name}</argument>
|
||||
<argument>${monitor_db_name}</argument>
|
||||
<argument>${wf:appPath()}/scripts/createMonitorDB.sql</argument>
|
||||
<file>monitor.sh</file>
|
||||
</shell>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -30,11 +30,16 @@ from rcount
|
|||
group by rcount.pid;
|
||||
|
||||
create view ${stats_db_name}.rndexpenditure as select * from stats_ext.rndexpediture;
|
||||
create view ${stats_db_name}.rndgdpexpenditure as select * from stats_ext.rndgdpexpenditure;
|
||||
create view ${stats_db_name}.doctoratestudents as select * from stats_ext.doctoratestudents;
|
||||
create view ${stats_db_name}.totalresearchers as select * from stats_ext.totalresearchers;
|
||||
create view ${stats_db_name}.totalresearchersft as select * from stats_ext.totalresearchersft;
|
||||
create view ${stats_db_name}.hrrst as select * from stats_ext.hrrst;
|
||||
|
||||
create table ${stats_db_name}.result_instance stored as parquet as
|
||||
select distinct r.*
|
||||
from (
|
||||
select substr(r.id, 4) as id, inst.accessright.classname as accessright, substr(inst.collectedfrom.key, 4) as collectedfrom,
|
||||
select substr(r.id, 4) as id, inst.accessright.classname as accessright, inst.accessright.openaccessroute as accessright_uw, substr(inst.collectedfrom.key, 4) as collectedfrom,
|
||||
substr(inst.hostedby.key, 4) as hostedby, inst.dateofacceptance.value as dateofacceptance, inst.license.value as license, p.qualifier.classname as pidtype, p.value as pid
|
||||
from ${openaire_db_name}.result r lateral view explode(r.instance) instances as inst lateral view explode(inst.pid) pids as p) r
|
||||
join ${stats_db_name}.result res on res.id=r.id;
|
||||
|
|
|
|||
|
|
@ -10,6 +10,11 @@ create view if not exists TARGET.creation_date as select * from SOURCE.creation_
|
|||
create view if not exists TARGET.funder as select * from SOURCE.funder;
|
||||
create view if not exists TARGET.fundref as select * from SOURCE.fundref;
|
||||
create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture;
|
||||
create view if not exists TARGET.rndgdpexpenditure as select * from SOURCE.rndgdpexpenditure;
|
||||
create view if not exists TARGET.doctoratestudents as select * from SOURCE.doctoratestudents;
|
||||
create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers;
|
||||
create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft;
|
||||
create view if not exists TARGET.hrrst as select * from SOURCE.hrrst;
|
||||
|
||||
create table TARGET.result stored as parquet as
|
||||
select distinct * from (
|
||||
|
|
@ -50,8 +55,16 @@ create table TARGET.result stored as parquet as
|
|||
'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech
|
||||
'openorgs____::e15adb13c4dadd49de4d35c39b5da93a', -- Nanyang Technological University
|
||||
'openorgs____::4b34103bde246228fcd837f5f1bf4212', -- Autonomous University of Barcelona
|
||||
'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb' -- McMaster University
|
||||
) )) foo;
|
||||
'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb', -- McMaster University
|
||||
'openorgs____::51c7fc556e46381734a25a6fbc3fd398', -- University of Modena and Reggio Emilia
|
||||
'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db', -- Bilkent University
|
||||
'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06', -- Saints Cyril and Methodius University of Skopje
|
||||
'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan
|
||||
'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork
|
||||
'openorgs____::38d7097854736583dde879d12dacafca', -- Brown University
|
||||
'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech
|
||||
'openorgs____::2530baca8a15936ba2e3297f2bce2e7e' -- University of Cape Town
|
||||
))) foo;
|
||||
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);
|
||||
|
|
|
|||
|
|
@ -70,7 +70,40 @@
|
|||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="Step1"/>
|
||||
<start to="resume_from"/>
|
||||
|
||||
<decision name="resume_from">
|
||||
<switch>
|
||||
<case to="Step1">${wf:conf('resumeFrom') eq 'Step1'}</case>
|
||||
<case to="Step2">${wf:conf('resumeFrom') eq 'Step2'}</case>
|
||||
<case to="Step3">${wf:conf('resumeFrom') eq 'Step3'}</case>
|
||||
<case to="Step4">${wf:conf('resumeFrom') eq 'Step4'}</case>
|
||||
<case to="Step5">${wf:conf('resumeFrom') eq 'Step5'}</case>
|
||||
<case to="Step6">${wf:conf('resumeFrom') eq 'Step6'}</case>
|
||||
<case to="Step7">${wf:conf('resumeFrom') eq 'Step7'}</case>
|
||||
<case to="Step8">${wf:conf('resumeFrom') eq 'Step8'}</case>
|
||||
<case to="Step9">${wf:conf('resumeFrom') eq 'Step9'}</case>
|
||||
<case to="Step10">${wf:conf('resumeFrom') eq 'Step10'}</case>
|
||||
<case to="Step11">${wf:conf('resumeFrom') eq 'Step11'}</case>
|
||||
<case to="Step12">${wf:conf('resumeFrom') eq 'Step12'}</case>
|
||||
<case to="Step13">${wf:conf('resumeFrom') eq 'Step13'}</case>
|
||||
<case to="Step14">${wf:conf('resumeFrom') eq 'Step14'}</case>
|
||||
<case to="Step15">${wf:conf('resumeFrom') eq 'Step15'}</case>
|
||||
<case to="Step15_5">${wf:conf('resumeFrom') eq 'Step15_5'}</case>
|
||||
<case to="Contexts">${wf:conf('resumeFrom') eq 'Contexts'}</case>
|
||||
<case to="Step16-createIndicatorsTables">${wf:conf('resumeFrom') eq 'Step16-createIndicatorsTables'}</case>
|
||||
<case to="Step16_1-definitions">${wf:conf('resumeFrom') eq 'Step16_1-definitions'}</case>
|
||||
<case to="Step16_5">${wf:conf('resumeFrom') eq 'Step16_5'}</case>
|
||||
<case to="Step19-finalize">${wf:conf('resumeFrom') eq 'Step19-finalize'}</case>
|
||||
<case to="step20-createMonitorDB">${wf:conf('resumeFrom') eq 'step20-createMonitorDB'}</case>
|
||||
<case to="step21-createObservatoryDB-pre">${wf:conf('resumeFrom') eq 'step21-createObservatoryDB-pre'}</case>
|
||||
<case to="step21-createObservatoryDB">${wf:conf('resumeFrom') eq 'step21-createObservatoryDB'}</case>
|
||||
<case to="step21-createObservatoryDB-post">${wf:conf('resumeFrom') eq 'step21-createObservatoryDB-post'}</case>
|
||||
<case to="Step22">${wf:conf('resumeFrom') eq 'Step22'}</case>
|
||||
<default to="Step1"/>
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
|
|
|
|||
2
pom.xml
2
pom.xml
|
|
@ -807,7 +807,7 @@
|
|||
<mockito-core.version>3.3.3</mockito-core.version>
|
||||
<mongodb.driver.version>3.4.2</mongodb.driver.version>
|
||||
<vtd.version>[2.12,3.0)</vtd.version>
|
||||
<dhp-schemas.version>[3.15.0]</dhp-schemas.version>
|
||||
<dhp-schemas.version>[3.15.1-SNAPSHOT]</dhp-schemas.version>
|
||||
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.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>
|
||||
|
|
|
|||
Loading…
Reference in New Issue