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refactoring

This commit is contained in:
Miriam Baglioni 2020-11-25 18:23:28 +01:00
parent 1a89f8211c
commit 124591a7f3
6 changed files with 188 additions and 186 deletions
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1
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java
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@ -26,7 +26,6 @@ public class Constants {
public static String ORCID = "orcid";
static {
accessRightsCoarMap.put("OPEN", "c_abf2");
accessRightsCoarMap.put("RESTRICTED", "c_16ec");

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java
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@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.*;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
@ -20,6 +19,7 @@ import eu.dnetlib.dhp.oa.graph.dump.Constants;
import eu.dnetlib.dhp.oa.graph.dump.ResultMapper;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import eu.dnetlib.dhp.schema.dump.oaf.community.Project;
import eu.dnetlib.dhp.schema.oaf.Relation;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java
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@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
@ -21,6 +20,7 @@ import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Constants;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import scala.Tuple2;

2
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java
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@ -164,7 +164,7 @@ public class CreateEntityTest {
final Consumer<ContextInfo> consumer = ci -> cInfoList.add(ci);
queryInformationSystem.getContextInformation(consumer);
for(ContextInfo cInfo: cInfoList){
for (ContextInfo cInfo : cInfoList) {
writer.write(new Gson().toJson(Process.getEntity(cInfo)));
}
writer.close();

22
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java
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@ -1,9 +1,11 @@
package eu.dnetlib.dhp.oa.graph.dump.funderresult;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Result;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.HashMap;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
@ -17,10 +19,11 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.HashMap;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Result;
public class ResultLinkedToProjectTest {
@ -38,7 +41,8 @@ public class ResultLinkedToProjectTest {
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName());
.createTempDirectory(
eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();

37
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java
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@ -1,11 +1,10 @@
package eu.dnetlib.dhp.oa.graph.dump.funderresult;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit;
import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
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;
@ -19,9 +18,13 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit;
import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
public class SplitPerFunderTest {
@ -64,12 +67,10 @@ public class SplitPerFunderTest {
@Test
public void test1() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump")
.getPath();
SparkDumpFunderResults.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/split",
@ -78,7 +79,6 @@ public class SplitPerFunderTest {
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
// FP7 3
@ -95,44 +95,43 @@ public class SplitPerFunderTest {
.assertEquals(
1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count());
// CIHR 2
tmp = sc
.textFile(workingDir.toString() + "/split/CIHR")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
Assertions.assertEquals(2, tmp.count());
//NWO 1
// NWO 1
tmp = sc
.textFile(workingDir.toString() + "/split/NWO")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
Assertions.assertEquals(1, tmp.count());
//NIH 3
// NIH 3
tmp = sc
.textFile(workingDir.toString() + "/split/NIH")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
Assertions.assertEquals(2, tmp.count());
//NSF 1
// NSF 1
tmp = sc
.textFile(workingDir.toString() + "/split/NSF")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
Assertions.assertEquals(1, tmp.count());
//SNSF 1
// SNSF 1
tmp = sc
.textFile(workingDir.toString() + "/split/SNSF")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
Assertions.assertEquals(1, tmp.count());
//NHMRC 1
// NHMRC 1
tmp = sc
.textFile(workingDir.toString() + "/split/NHMRC")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
Assertions.assertEquals(1, tmp.count());
//H2020 3
// H2020 3
tmp = sc
.textFile(workingDir.toString() + "/split/EC_H2020")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));