2020-06-15 11:13:51 +02:00
|
|
|
|
2020-06-15 11:06:18 +02:00
|
|
|
package eu.dnetlib.dhp.oa.graph.dump;
|
|
|
|
|
2020-06-15 11:13:51 +02:00
|
|
|
import java.io.IOException;
|
|
|
|
import java.nio.file.Files;
|
|
|
|
import java.nio.file.Path;
|
|
|
|
import java.util.Arrays;
|
|
|
|
import java.util.HashMap;
|
|
|
|
import java.util.List;
|
|
|
|
|
|
|
|
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.Encoders;
|
|
|
|
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 org.slf4j.Logger;
|
|
|
|
import org.slf4j.LoggerFactory;
|
|
|
|
|
|
|
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
|
|
import com.google.gson.Gson;
|
|
|
|
|
|
|
|
import eu.dnetlib.dhp.schema.dump.oaf.Software;
|
|
|
|
|
2020-06-15 11:06:18 +02:00
|
|
|
public class SplitForCommunityTest {
|
2020-06-15 11:13:51 +02:00
|
|
|
|
|
|
|
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
|
|
|
|
|
|
|
private static SparkSession spark;
|
|
|
|
|
|
|
|
private static Path workingDir;
|
|
|
|
|
|
|
|
private static String MOCK_IS_LOOK_UP_URL = "BASEURL:8280/is/services/isLookUp";
|
|
|
|
|
|
|
|
private static final Logger log = LoggerFactory.getLogger(DumpJobTest.class);
|
|
|
|
|
|
|
|
private static HashMap<String, String> map = new HashMap<>();
|
|
|
|
|
|
|
|
static {
|
|
|
|
map.put("egi", "EGI Federation");
|
|
|
|
map.put("fet-fp7", "FET FP7");
|
|
|
|
map.put("fet-h2020", "FET H2020");
|
|
|
|
map.put("clarin", "CLARIN");
|
|
|
|
map.put("fam", "Fisheries and Aquaculture Management");
|
|
|
|
map.put("ni", "Neuroinformatics");
|
|
|
|
map.put("mes", "European Marine Scinece");
|
|
|
|
map.put("instruct", "Instruct-Eric");
|
|
|
|
map.put("rda", "Research Data Alliance");
|
|
|
|
map.put("elixir-gr", "ELIXIR GR");
|
|
|
|
map.put("aginfra", "Agricultural and Food Sciences");
|
|
|
|
map.put("dariah", "DARIAH EU");
|
|
|
|
map.put("risis", "RISI");
|
|
|
|
map.put("ee", "SDSN - Greece");
|
|
|
|
map.put("oa-pg", "EC Post-Grant Open Access Pilot");
|
|
|
|
map.put("beopen", "Transport Research");
|
|
|
|
map.put("euromarine", "Euromarine");
|
|
|
|
map.put("ifremer", "Ifremer");
|
|
|
|
map.put("dh-ch", "Digital Humanities and Cultural Heritage");
|
|
|
|
map.put("science-innovation-policy", "Science and Innovation Policy Studies");
|
|
|
|
map.put("covid-19", "COVID-19");
|
|
|
|
map.put("enrmaps", "Energy Research");
|
|
|
|
map.put("epos", "EPOS");
|
|
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
// @Mock
|
|
|
|
// private SparkDumpCommunityProducts dumpCommunityProducts;
|
|
|
|
|
|
|
|
// private QueryInformationSystem queryInformationSystem;
|
|
|
|
|
|
|
|
// @Mock
|
|
|
|
// private ISLookUpService isLookUpService;
|
|
|
|
|
|
|
|
List<String> communityMap = Arrays
|
|
|
|
.asList(
|
|
|
|
"<community id=\"egi\" label=\"EGI Federation\"/>",
|
|
|
|
"<community id=\"fet-fp7\" label=\"FET FP7\"/>",
|
|
|
|
"<community id=\"fet-h2020\" label=\"FET H2020\"/>",
|
|
|
|
"<community id=\"clarin\" label=\"CLARIN\"/>",
|
|
|
|
"<community id=\"rda\" label=\"Research Data Alliance\"/>",
|
|
|
|
"<community id=\"ee\" label=\"SDSN - Greece\"/>",
|
|
|
|
"<community id=\"dh-ch\" label=\"Digital Humanities and Cultural Heritage\"/>",
|
|
|
|
"<community id=\"fam\" label=\"Fisheries and Aquaculture Management\"/>",
|
|
|
|
"<community id=\"ni\" label=\"Neuroinformatics\"/>",
|
|
|
|
"<community id=\"mes\" label=\"European Marine Science\"/>",
|
|
|
|
"<community id=\"instruct\" label=\"Instruct-ERIC\"/>",
|
|
|
|
"<community id=\"elixir-gr\" label=\"ELIXIR GR\"/>",
|
|
|
|
"<community id=\"aginfra\" label=\"Agricultural and Food Sciences\"/>",
|
|
|
|
"<community id=\"dariah\" label=\"DARIAH EU\"/>",
|
|
|
|
"<community id=\"risis\" label=\"RISIS\"/>",
|
|
|
|
"<community id=\"epos\" label=\"EPOS\"/>",
|
|
|
|
"<community id=\"beopen\" label=\"Transport Research\"/>",
|
|
|
|
"<community id=\"euromarine\" label=\"EuroMarine\"/>",
|
|
|
|
"<community id=\"ifremer\" label=\"Ifremer\"/>",
|
|
|
|
"<community id=\"oa-pg\" label=\"EC Post-Grant Open Access Pilot\"/>",
|
|
|
|
"<community id=\"science-innovation-policy\" label=\"Science and Innovation Policy Studies\"/>",
|
|
|
|
"<community id=\"covid-19\" label=\"COVID-19\"/>",
|
|
|
|
"<community id=\"enermaps\" label=\"Energy Research\"/>");
|
|
|
|
|
|
|
|
private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
|
|
|
|
+
|
|
|
|
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
|
|
|
|
" return " +
|
|
|
|
"<community> " +
|
|
|
|
"{$x//CONFIGURATION/context/@id}" +
|
|
|
|
"{$x//CONFIGURATION/context/@label}" +
|
|
|
|
"</community>";
|
|
|
|
|
|
|
|
@BeforeAll
|
|
|
|
public static void beforeAll() throws IOException {
|
|
|
|
workingDir = Files.createTempDirectory(SplitForCommunityTest.class.getSimpleName());
|
|
|
|
log.info("using work dir {}", workingDir);
|
|
|
|
|
|
|
|
SparkConf conf = new SparkConf();
|
|
|
|
conf.setAppName(SplitForCommunityTest.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(SplitForCommunityTest.class.getSimpleName())
|
|
|
|
.config(conf)
|
|
|
|
.getOrCreate();
|
|
|
|
}
|
|
|
|
|
|
|
|
// @BeforeEach
|
|
|
|
// public void setUp() throws ISLookUpException {
|
|
|
|
// lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityMap);
|
|
|
|
// lenient().when(dumpCommunityProducts.getIsLookUpService(MOCK_IS_LOOK_UP_URL)).thenReturn(isLookUpService);
|
|
|
|
//
|
|
|
|
// }
|
|
|
|
|
|
|
|
@AfterAll
|
|
|
|
public static void afterAll() throws IOException {
|
|
|
|
FileUtils.deleteDirectory(workingDir.toFile());
|
|
|
|
spark.stop();
|
|
|
|
}
|
|
|
|
|
|
|
|
@Test
|
|
|
|
public void test1() throws Exception {
|
|
|
|
|
|
|
|
final String sourcePath = getClass()
|
|
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/splitForCommunity/software")
|
|
|
|
.getPath();
|
|
|
|
|
|
|
|
SparkSplitForCommunity.main(new String[] {
|
|
|
|
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
|
|
"-outputPath", workingDir.toString() + "/split",
|
|
|
|
"-sourcePath", sourcePath,
|
|
|
|
"-resultTableName", "eu.dnetlib.dhp.schema.dump.oaf.Software",
|
|
|
|
"-communityMap", new Gson().toJson(map)
|
|
|
|
});
|
|
|
|
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
|
|
|
|
JavaRDD<Software> tmp = sc
|
|
|
|
.textFile(workingDir.toString() + "/split/dh-ch")
|
|
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
|
|
|
|
|
|
|
|
org.apache.spark.sql.Dataset<Software> verificationDataset = spark
|
|
|
|
.createDataset(tmp.rdd(), Encoders.bean(Software.class));
|
|
|
|
|
|
|
|
Assertions.assertEquals(1, verificationDataset.count());
|
|
|
|
|
|
|
|
Assertions
|
|
|
|
.assertEquals(
|
|
|
|
1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
|
|
|
|
|
|
|
|
tmp = sc
|
|
|
|
.textFile(workingDir.toString() + "/split/egi")
|
|
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
|
|
|
|
|
|
|
|
verificationDataset = spark
|
|
|
|
.createDataset(tmp.rdd(), Encoders.bean(Software.class));
|
|
|
|
|
|
|
|
Assertions.assertEquals(1, verificationDataset.count());
|
|
|
|
|
|
|
|
Assertions
|
|
|
|
.assertEquals(
|
|
|
|
1, verificationDataset.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
|
|
|
|
|
|
|
|
tmp = sc
|
|
|
|
.textFile(workingDir.toString() + "/split/ni")
|
|
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
|
|
|
|
|
|
|
|
verificationDataset = spark
|
|
|
|
.createDataset(tmp.rdd(), Encoders.bean(Software.class));
|
|
|
|
|
|
|
|
Assertions.assertEquals(1, verificationDataset.count());
|
|
|
|
|
|
|
|
Assertions
|
|
|
|
.assertEquals(
|
|
|
|
1, verificationDataset.filter("id = '50|datacite____::6b1e3a2fa60ed8c27317a66d6357f795'").count());
|
|
|
|
|
|
|
|
tmp = sc
|
|
|
|
.textFile(workingDir.toString() + "/split/science-innovation-policy")
|
|
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
|
|
|
|
|
|
|
|
verificationDataset = spark
|
|
|
|
.createDataset(tmp.rdd(), Encoders.bean(Software.class));
|
|
|
|
|
|
|
|
Assertions.assertEquals(4, verificationDataset.count());
|
|
|
|
|
|
|
|
Assertions
|
|
|
|
.assertEquals(
|
|
|
|
1, verificationDataset.filter("id = '50|dedup_wf_001::0347b1cd516fc59e41ba92e0d74e4e9f'").count());
|
|
|
|
Assertions
|
|
|
|
.assertEquals(
|
|
|
|
1, verificationDataset.filter("id = '50|dedup_wf_001::1432beb6171baa5da8a85a7f99545d69'").count());
|
|
|
|
Assertions
|
|
|
|
.assertEquals(
|
|
|
|
1, verificationDataset.filter("id = '50|dedup_wf_001::1c8bd19e633976e314b88ce5c3f92d69'").count());
|
|
|
|
Assertions
|
|
|
|
.assertEquals(
|
|
|
|
1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
|
|
|
|
|
|
|
|
}
|
2020-06-15 11:06:18 +02:00
|
|
|
}
|