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refactoring

This commit is contained in:
Miriam Baglioni 2020-08-13 18:50:33 +02:00
parent a5043de5da
commit d2a8a4961a
1 changed files with 74 additions and 70 deletions
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144
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/RelationFromOrganizationTest.java
View File

@ -1,10 +1,11 @@
package eu.dnetlib.dhp.oa.graph.dump.graph; package eu.dnetlib.dhp.oa.graph.dump.graph;
import com.fasterxml.jackson.databind.ObjectMapper; import java.io.IOException;
import eu.dnetlib.dhp.oa.graph.dump.Utils; import java.nio.file.Files;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; import java.nio.file.Path;
import eu.dnetlib.dhp.utils.DHPUtils; import java.util.HashMap;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.neethi.Assertion; import org.apache.neethi.Assertion;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
@ -21,96 +22,99 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import java.io.IOException; import com.fasterxml.jackson.databind.ObjectMapper;
import java.nio.file.Files;
import java.nio.file.Path; import eu.dnetlib.dhp.oa.graph.dump.Utils;
import java.util.HashMap; import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation;
import eu.dnetlib.dhp.utils.DHPUtils;
public class RelationFromOrganizationTest { public class RelationFromOrganizationTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark; private static SparkSession spark;
private static Path workingDir; private static Path workingDir;
private static final Logger log = LoggerFactory private static final Logger log = LoggerFactory
.getLogger(RelationFromOrganizationTest.class); .getLogger(RelationFromOrganizationTest.class);
private static HashMap<String, String> map = new HashMap<>(); private static HashMap<String, String> map = new HashMap<>();
String organizationCommunityMap= "{\"20|grid________::afaa39865943381c51f76c08725ffa75\":[\"mes\",\"euromarine\"], \"20|corda__h2020::e8dbe14cca9bf6fce09d468872f813f8\":[\"mes\",\"euromarine\"], \"20|snsf________::9b253f265e3bef5cae6d881fdf61aceb\":[\"mes\",\"euromarine\"],\"20|rcuk________::e054eea0a47665af8c3656b5785ccf76\":[\"mes\",\"euromarine\"],\"20|corda__h2020::edc18d67c9b11fb616ca9f6e1db1b151\":[\"mes\",\"euromarine\"],\"20|rcuk________::d5736d9da90521ddcdc7828a05a85e9a\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f5d418d3aa1cf817ddefcc3fdc039f27\":[\"mes\",\"euromarine\"],\"20|snsf________::8fa091f8f25a846779acb4ea97b50aef\":[\"mes\",\"euromarine\"],\"20|corda__h2020::81e020977211c2c40fae2e1a50bffd71\":[\"mes\",\"euromarine\"],\"20|corda_______::81e020977211c2c40fae2e1a50bffd71\":[\"mes\",\"euromarine\"],\"20|snsf________::31d0a100e54e3cdb3c6f52d91e638c78\":[\"mes\",\"euromarine\"],\"20|corda__h2020::ea379ef91b8cc86f9ac5edc4169292db\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f75ee2ee48e5cb0ec8c8d30aaa8fef70\":[\"mes\",\"euromarine\"],\"20|rcuk________::e16010089551a1a9182a94604fc0ea59\":[\"mes\",\"euromarine\"],\"20|corda__h2020::38531a2cce7c5c347ffc439b07c1f43b\":[\"mes\",\"euromarine\"],\"20|corda_______::38531a2cce7c5c347ffc439b07c1f43b\":[\"mes\",\"euromarine\"],\"20|grid________::b2cbbf5eadbbf87d534b022bad3191d7\":[\"mes\",\"euromarine\"],\"20|snsf________::74730ef1439d7f7636a8be58a6b471b8\":[\"mes\",\"euromarine\"],\"20|nsf_________::ad72e19043a5a467e35f9b444d11563e\":[\"mes\",\"euromarine\"],\"20|rcuk________::0fc3e92500290902a2d38ec2445e74c3\":[\"mes\",\"euromarine\"],\"20|grid________::ad2c29905da0eb3c06b3fa80cacd89ea\":[\"mes\",\"euromarine\"],\"20|corda__h2020::30b53e4d63d3724f00acb9cbaca40860\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f60f84bee14ad93f0db0e49af1d5c317\":[\"mes\",\"euromarine\"], \"20|corda__h2020::7bf251ac3765b5e89d82270a1763d09f\":[\"mes\",\"euromarine\"], \"20|corda__h2020::65531bd11be9935948c7f2f4db1c1832\":[\"mes\",\"euromarine\"], \"20|corda__h2020::e0e98f86bbc76638bbb72a8fe2302946\":[\"mes\",\"euromarine\"], \"20|snsf________::3eb43582ac27601459a8d8b3e195724b\":[\"mes\",\"euromarine\"], \"20|corda__h2020::af2481dab65d06c8ea0ae02b5517b9b6\":[\"mes\",\"euromarine\"], \"20|corda__h2020::c19d05cfde69a50d3ebc89bd0ee49929\":[\"mes\",\"euromarine\"], \"20|corda__h2020::af0bfd9fc09f80d9488f56d71a9832f0\":[\"mes\",\"euromarine\"], \"20|rcuk________::f33c02afb0dc66c49d0ed97ca5dd5cb0\":[\"beopen\"], " + String organizationCommunityMap = "{\"20|grid________::afaa39865943381c51f76c08725ffa75\":[\"mes\",\"euromarine\"], \"20|corda__h2020::e8dbe14cca9bf6fce09d468872f813f8\":[\"mes\",\"euromarine\"], \"20|snsf________::9b253f265e3bef5cae6d881fdf61aceb\":[\"mes\",\"euromarine\"],\"20|rcuk________::e054eea0a47665af8c3656b5785ccf76\":[\"mes\",\"euromarine\"],\"20|corda__h2020::edc18d67c9b11fb616ca9f6e1db1b151\":[\"mes\",\"euromarine\"],\"20|rcuk________::d5736d9da90521ddcdc7828a05a85e9a\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f5d418d3aa1cf817ddefcc3fdc039f27\":[\"mes\",\"euromarine\"],\"20|snsf________::8fa091f8f25a846779acb4ea97b50aef\":[\"mes\",\"euromarine\"],\"20|corda__h2020::81e020977211c2c40fae2e1a50bffd71\":[\"mes\",\"euromarine\"],\"20|corda_______::81e020977211c2c40fae2e1a50bffd71\":[\"mes\",\"euromarine\"],\"20|snsf________::31d0a100e54e3cdb3c6f52d91e638c78\":[\"mes\",\"euromarine\"],\"20|corda__h2020::ea379ef91b8cc86f9ac5edc4169292db\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f75ee2ee48e5cb0ec8c8d30aaa8fef70\":[\"mes\",\"euromarine\"],\"20|rcuk________::e16010089551a1a9182a94604fc0ea59\":[\"mes\",\"euromarine\"],\"20|corda__h2020::38531a2cce7c5c347ffc439b07c1f43b\":[\"mes\",\"euromarine\"],\"20|corda_______::38531a2cce7c5c347ffc439b07c1f43b\":[\"mes\",\"euromarine\"],\"20|grid________::b2cbbf5eadbbf87d534b022bad3191d7\":[\"mes\",\"euromarine\"],\"20|snsf________::74730ef1439d7f7636a8be58a6b471b8\":[\"mes\",\"euromarine\"],\"20|nsf_________::ad72e19043a5a467e35f9b444d11563e\":[\"mes\",\"euromarine\"],\"20|rcuk________::0fc3e92500290902a2d38ec2445e74c3\":[\"mes\",\"euromarine\"],\"20|grid________::ad2c29905da0eb3c06b3fa80cacd89ea\":[\"mes\",\"euromarine\"],\"20|corda__h2020::30b53e4d63d3724f00acb9cbaca40860\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f60f84bee14ad93f0db0e49af1d5c317\":[\"mes\",\"euromarine\"], \"20|corda__h2020::7bf251ac3765b5e89d82270a1763d09f\":[\"mes\",\"euromarine\"], \"20|corda__h2020::65531bd11be9935948c7f2f4db1c1832\":[\"mes\",\"euromarine\"], \"20|corda__h2020::e0e98f86bbc76638bbb72a8fe2302946\":[\"mes\",\"euromarine\"], \"20|snsf________::3eb43582ac27601459a8d8b3e195724b\":[\"mes\",\"euromarine\"], \"20|corda__h2020::af2481dab65d06c8ea0ae02b5517b9b6\":[\"mes\",\"euromarine\"], \"20|corda__h2020::c19d05cfde69a50d3ebc89bd0ee49929\":[\"mes\",\"euromarine\"], \"20|corda__h2020::af0bfd9fc09f80d9488f56d71a9832f0\":[\"mes\",\"euromarine\"], \"20|rcuk________::f33c02afb0dc66c49d0ed97ca5dd5cb0\":[\"beopen\"], "
"\"20|grid________::a867f78acdc5041b34acfe4f9a349157\":[\"beopen\"], \"20|grid________::7bb116a1a9f95ab812bf9d2dea2be1ff\":[\"beopen\"], \"20|corda__h2020::6ab0e0739dbe625b99a2ae45842164ad\":[\"beopen\"], \"20|corda__h2020::8ba50792bc5f4d51d79fca47d860c602\":[\"beopen\"], \"20|corda_______::8ba50792bc5f4d51d79fca47d860c602\":[\"beopen\"], \"20|corda__h2020::e70e9114979e963eef24666657b807c3\":[\"beopen\"], \"20|corda_______::e70e9114979e963eef24666657b807c3\":[\"beopen\"], \"20|corda_______::15911e01e9744d57205825d77c218737\":[\"beopen\"], \"20|opendoar____::056a41e24e2a9a67215e87bbee6a80ab\":[\"beopen\"], \"20|opendoar____::7f67f2e6c6fbb0628f8160fcd3d92ae3\":[\"beopen\"], \"20|grid________::a8ecfd7c084e561168bcbe6bf0daf3e3\":[\"beopen\"], \"20|corda_______::7bbe6cc5d8ec1864739a04b0d020c9e9\":[\"beopen\"], \"20|corda_______::3ff558e30c2e434d688539548300b050\":[\"beopen\"], \"20|corda__h2020::5ffee5b3b83b33a8cf0e046877bd3a39\":[\"beopen\"], \"20|corda__h2020::5187217e2e806a6df3579c46f82401bc\":[\"beopen\"], \"20|grid________::5fa7e2709bcd945e26bfa18689adeec1\":[\"beopen\"], \"20|corda_______::d8696683c53027438031a96ad27c3c07\":[\"beopen\"], \"20|corda__h2020::d8696683c53027438031a96ad27c3c07\":[\"beopen\"], \"20|rcuk________::23a79ebdfa59790864e4a485881568c1\":[\"beopen\"], \"20|corda__h2020::b76cf8fe49590a966953c37e18608af9\":[\"beopen\"], \"20|grid________::d2f0204126ee709244a488a4cd3b91c2\":[\"beopen\"], \"20|corda__h2020::05aba9d2ed17533d15221e5655ac11e6\":[\"beopen\"], \"20|grid________::802401579481dc32062bdee69f5e6a34\":[\"beopen\"], \"20|corda__h2020::3f6d9d54cac975a517ba6b252c81582d\":[\"beopen\"]}"; +
"\"20|grid________::a867f78acdc5041b34acfe4f9a349157\":[\"beopen\"], \"20|grid________::7bb116a1a9f95ab812bf9d2dea2be1ff\":[\"beopen\"], \"20|corda__h2020::6ab0e0739dbe625b99a2ae45842164ad\":[\"beopen\"], \"20|corda__h2020::8ba50792bc5f4d51d79fca47d860c602\":[\"beopen\"], \"20|corda_______::8ba50792bc5f4d51d79fca47d860c602\":[\"beopen\"], \"20|corda__h2020::e70e9114979e963eef24666657b807c3\":[\"beopen\"], \"20|corda_______::e70e9114979e963eef24666657b807c3\":[\"beopen\"], \"20|corda_______::15911e01e9744d57205825d77c218737\":[\"beopen\"], \"20|opendoar____::056a41e24e2a9a67215e87bbee6a80ab\":[\"beopen\"], \"20|opendoar____::7f67f2e6c6fbb0628f8160fcd3d92ae3\":[\"beopen\"], \"20|grid________::a8ecfd7c084e561168bcbe6bf0daf3e3\":[\"beopen\"], \"20|corda_______::7bbe6cc5d8ec1864739a04b0d020c9e9\":[\"beopen\"], \"20|corda_______::3ff558e30c2e434d688539548300b050\":[\"beopen\"], \"20|corda__h2020::5ffee5b3b83b33a8cf0e046877bd3a39\":[\"beopen\"], \"20|corda__h2020::5187217e2e806a6df3579c46f82401bc\":[\"beopen\"], \"20|grid________::5fa7e2709bcd945e26bfa18689adeec1\":[\"beopen\"], \"20|corda_______::d8696683c53027438031a96ad27c3c07\":[\"beopen\"], \"20|corda__h2020::d8696683c53027438031a96ad27c3c07\":[\"beopen\"], \"20|rcuk________::23a79ebdfa59790864e4a485881568c1\":[\"beopen\"], \"20|corda__h2020::b76cf8fe49590a966953c37e18608af9\":[\"beopen\"], \"20|grid________::d2f0204126ee709244a488a4cd3b91c2\":[\"beopen\"], \"20|corda__h2020::05aba9d2ed17533d15221e5655ac11e6\":[\"beopen\"], \"20|grid________::802401579481dc32062bdee69f5e6a34\":[\"beopen\"], \"20|corda__h2020::3f6d9d54cac975a517ba6b252c81582d\":[\"beopen\"]}";
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(RelationFromOrganizationTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
@BeforeAll SparkConf conf = new SparkConf();
public static void beforeAll() throws IOException { conf.setAppName(RelationFromOrganizationTest.class.getSimpleName());
workingDir = Files
.createTempDirectory(RelationFromOrganizationTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf(); conf.setMaster("local[*]");
conf.setAppName(RelationFromOrganizationTest.class.getSimpleName()); 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());
conf.setMaster("local[*]"); spark = SparkSession
conf.set("spark.driver.host", "localhost"); .builder()
conf.set("hive.metastore.local", "true"); .appName(RelationFromOrganizationTest.class.getSimpleName())
conf.set("spark.ui.enabled", "false"); .config(conf)
conf.set("spark.sql.warehouse.dir", workingDir.toString()); .getOrCreate();
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); }
spark = SparkSession @AfterAll
.builder() public static void afterAll() throws IOException {
.appName(RelationFromOrganizationTest.class.getSimpleName()) FileUtils.deleteDirectory(workingDir.toFile());
.config(conf) spark.stop();
.getOrCreate(); }
}
@AfterAll @Test
public static void afterAll() throws IOException { public void test1() throws Exception {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test final String sourcePath = getClass()
public void test1() throws Exception { .getResource("/eu/dnetlib/dhp/oa/graph/dump/graph/relation")
.getPath();
final String sourcePath = getClass() SparkOrganizationRelation.main(new String[] {
.getResource("/eu/dnetlib/dhp/oa/graph/dump/graph/relation") "-isSparkSessionManaged", Boolean.FALSE.toString(),
.getPath(); "-outputPath", workingDir.toString() + "/relation",
"-sourcePath", sourcePath,
"-organizationCommunityMap", organizationCommunityMap
});
SparkOrganizationRelation.main(new String[]{ final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/relation",
"-sourcePath", sourcePath,
"-organizationCommunityMap", organizationCommunityMap
});
JavaRDD<Relation> tmp = sc
.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); org.apache.spark.sql.Dataset<Relation> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
JavaRDD<Relation> tmp = sc verificationDataset.createOrReplaceTempView("table");
.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
org.apache.spark.sql.Dataset<Relation> verificationDataset = spark Assertions.assertEquals(170, verificationDataset.count());
.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
verificationDataset.createOrReplaceTempView("table"); Dataset<Row> checkDs = spark
.sql(
"Select source.id, source.type " +
"from table ");
Assertions.assertEquals(170, verificationDataset.count()); Assertions.assertEquals(2, checkDs.filter("substr(id, 4, 5) = 'dedup' ").count());
Dataset<Row> checkDs = spark.sql("Select source.id, source.type " + Assertions.assertEquals(0, checkDs.filter("id = '20|grid________::afaa39865943381c51f76c08725ffa75'").count());
"from table ");
Assertions.assertEquals(2, checkDs.filter("substr(id, 4, 5) = 'dedup' ").count()); Assertions.assertEquals(25, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("beopen") + "'").count());
Assertions.assertEquals(0, checkDs.filter("id = '20|grid________::afaa39865943381c51f76c08725ffa75'").count()); Assertions
.assertEquals(30, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("euromarine") + "'").count());
Assertions.assertEquals(25, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("beopen") + "'").count()); Assertions.assertEquals(30, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("mes") + "'").count());
}
Assertions.assertEquals(30, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("euromarine") + "'").count()); }
Assertions.assertEquals(30, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("mes") + "'").count());
}
}