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Merging different compatibility levels (pinocchio operator) #47

Manually merged
alessia.bardi merged 2 commits from merge_graph into master 2020-10-09 14:44:52 +02:00
Conversation 0 Commits 2 Files Changed 13 +226 -2
13 changed files with 226 additions and 2 deletions
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97
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/DatasourceCompatibilityComparator.java Normal file
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@ -0,0 +1,97 @@
package eu.dnetlib.dhp.oa.graph.merge;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class DatasourceCompatibilityComparator implements Comparator<Qualifier> {
@Override
public int compare(Qualifier left, Qualifier right) {
String lClass = left.getClassid();
String rClass = right.getClassid();
if (lClass.equals(rClass))
return 0;
if (lClass.equals("openaire-cris_1.1"))
return -1;
if (rClass.equals("openaire-cris_1.1"))
return 1;
if (lClass.equals("openaire4.0"))
return -1;
if (rClass.equals("openaire4.0"))
return 1;
if (lClass.equals("driver-openaire2.0"))
return -1;
if (rClass.equals("driver-openaire2.0"))
return 1;
if (lClass.equals("driver"))
return -1;
if (rClass.equals("driver"))
return 1;
if (lClass.equals("openaire2.0"))
return -1;
if (rClass.equals("openaire2.0"))
return 1;
if (lClass.equals("openaire3.0"))
return -1;
if (rClass.equals("openaire3.0"))
return 1;
if (lClass.equals("openaire2.0_data"))
return -1;
if (rClass.equals("openaire2.0_data"))
return 1;
if (lClass.equals("native"))
return -1;
if (rClass.equals("native"))
return 1;
if (lClass.equals("hostedBy"))
return -1;
if (rClass.equals("hostedBy"))
return 1;
if (lClass.equals("notCompatible"))
return -1;
if (rClass.equals("notCompatible"))
return 1;
if (lClass.equals("UNKNOWN"))
return -1;
if (rClass.equals("UNKNOWN"))
return 1;
// Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass);
}
/*
* CASE WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY
* ['openaire-cris_1.1']) THEN 'openaire-cris_1.1@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT
* COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['openaire4.0']) THEN
* 'openaire4.0@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override,
* a.compatibility):: TEXT) @> ARRAY ['driver', 'openaire2.0']) THEN
* 'driver-openaire2.0@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE
* (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['driver']) THEN
* 'driver@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override,
* a.compatibility) :: TEXT) @> ARRAY ['openaire2.0']) THEN 'openaire2.0@@@dnet:datasourceCompatibilityLevel' WHEN
* (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['openaire3.0']) THEN
* 'openaire3.0@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override,
* a.compatibility) :: TEXT) @> ARRAY ['openaire2.0_data']) THEN
* 'openaire2.0_data@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE
* (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['native']) THEN
* 'native@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override,
* a.compatibility) :: TEXT) @> ARRAY ['hostedBy']) THEN 'hostedBy@@@dnet:datasourceCompatibilityLevel' WHEN
* (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['notCompatible'])
* THEN 'notCompatible@@@dnet:datasourceCompatibilityLevel' ELSE 'UNKNOWN@@@dnet:datasourceCompatibilityLevel' END
*/
}

37
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphSparkJob.java
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@ -3,8 +3,9 @@ package eu.dnetlib.dhp.oa.graph.merge;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Objects;
import java.util.Optional;
import java.util.*;
import javax.xml.crypto.Data;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
@ -14,6 +15,7 @@ import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -39,6 +41,14 @@ public class MergeGraphSparkJob {
private static final String PRIORITY_DEFAULT = "BETA"; // BETA | PROD
private static final Datasource DATASOURCE = new Datasource();
static {
Qualifier compatibility = new Qualifier();
compatibility.setClassid("UNKNOWN");
DATASOURCE.setOpenairecompatibility(compatibility);
}
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
@ -104,6 +114,10 @@ public class MergeGraphSparkJob {
.map((MapFunction<Tuple2<Tuple2<String, P>, Tuple2<String, B>>, P>) value -> {
Optional<P> p = Optional.ofNullable(value._1()).map(Tuple2::_2);
Optional<B> b = Optional.ofNullable(value._2()).map(Tuple2::_2);
if (p.orElse((P) b.orElse((B) DATASOURCE)) instanceof Datasource) {
return mergeDatasource(p, b);
}
switch (priority) {
default:
case "BETA":
@ -119,6 +133,25 @@ public class MergeGraphSparkJob {
.json(outputPath);
}
protected static <P extends Oaf, B extends Oaf> P mergeDatasource(Optional<P> p, Optional<B> b) {
if (p.isPresent() & !b.isPresent()) {
return p.get();
}
if (b.isPresent() & !p.isPresent()) {
return (P) b.get();
}
if (!b.isPresent() & !p.isPresent()) {
return null; // unlikely, at least one should be produced by the join operation
}
Datasource dp = (Datasource) p.get();
Datasource db = (Datasource) b.get();
List<Qualifier> list = Arrays.asList(dp.getOpenairecompatibility(), db.getOpenairecompatibility());
dp.setOpenairecompatibility(Collections.min(list, new DatasourceCompatibilityComparator()));
return (P) dp;
}
private static <P extends Oaf, B extends Oaf> P mergeWithPriorityToPROD(Optional<P> p, Optional<B> b) {
if (b.isPresent() & !p.isPresent()) {
return (P) b.get();

84
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphSparkJobTest.java Normal file
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@ -0,0 +1,84 @@
package eu.dnetlib.dhp.oa.graph.merge;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Datasource;
public class MergeGraphSparkJobTest {
private ObjectMapper mapper;
@BeforeEach
public void setUp() {
mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
}
@Test
public void testMergeDatasources() throws IOException {
assertEquals(
"openaire-cris_1.1",
MergeGraphSparkJob
.mergeDatasource(
d("datasource_cris.json"),
d("datasource_UNKNOWN.json"))
.getOpenairecompatibility()
.getClassid());
assertEquals(
"openaire-cris_1.1",
MergeGraphSparkJob
.mergeDatasource(
d("datasource_UNKNOWN.json"),
d("datasource_cris.json"))
.getOpenairecompatibility()
.getClassid());
assertEquals(
"driver-openaire2.0",
MergeGraphSparkJob
.mergeDatasource(
d("datasource_native.json"),
d("datasource_driver-openaire2.0.json"))
.getOpenairecompatibility()
.getClassid());
assertEquals(
"driver-openaire2.0",
MergeGraphSparkJob
.mergeDatasource(
d("datasource_driver-openaire2.0.json"),
d("datasource_native.json"))
.getOpenairecompatibility()
.getClassid());
assertEquals(
"openaire4.0",
MergeGraphSparkJob
.mergeDatasource(
d("datasource_notCompatible.json"),
d("datasource_openaire4.0.json"))
.getOpenairecompatibility()
.getClassid());
assertEquals(
"notCompatible",
MergeGraphSparkJob
.mergeDatasource(
d("datasource_notCompatible.json"),
d("datasource_UNKNOWN.json"))
.getOpenairecompatibility()
.getClassid());
}
private Optional<Datasource> d(String file) throws IOException {
String json = IOUtils.toString(getClass().getResourceAsStream(file));
return Optional.of(mapper.readValue(json, Datasource.class));
}
}

1
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_UNKNOWN.json Normal file
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@ -0,0 +1 @@
{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "UNKNOWN" }}

1
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_cris.json Normal file
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@ -0,0 +1 @@
{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "openaire-cris_1.1" }}

1
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_driver-openaire2.0.json Normal file
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@ -0,0 +1 @@
{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "driver-openaire2.0" }}

1
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_hostedby.json Normal file
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@ -0,0 +1 @@
{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "hostedBy" }}

1
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_native.json Normal file
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@ -0,0 +1 @@
{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "native" }}

1
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_notCompatible.json Normal file
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@ -0,0 +1 @@
{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "notCompatible" }}

1
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_openaire2.0.json Normal file
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@ -0,0 +1 @@
{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "openaire2.0" }}

1
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_openaire2.0_data.json Normal file
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@ -0,0 +1 @@
{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "openaire2.0_data" }}

1
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_openaire3.0.json Normal file
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@ -0,0 +1 @@
{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "openaire3.0" }}

1
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_openaire4.0.json Normal file
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@ -0,0 +1 @@
{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "openaire4.0" }}