From edddfc6c637d601823681c190305aa1105ee5834 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 21 Jun 2022 18:28:53 +0200 Subject: [PATCH] [DUMP DELTA PROJECTS] adding test and resource --- .../projectssubset/ProjectSubsetTest.java | 118 ++++++++++++++++++ .../graph/dump/projectsubset/allnew/projects | 12 ++ .../dump/projectsubset/matchOne/projects | 12 ++ .../dhp/oa/graph/dump/projectsubset/projectId | 28 +++++ 4 files changed, 170 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java new file mode 100644 index 000000000..d5b1ce776 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java @@ -0,0 +1,118 @@ +package eu.dnetlib.dhp.oa.graph.dump.projectssubset; +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; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SaveMode; +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 eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; +public class ProjectSubsetTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static SparkSession spark; + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); + private static final HashMap map = new HashMap<>(); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.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(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + @Test + void testAllNew() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(12, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(1, tmp.filter(p -> p.getId().substring(3, 15).equals("corda_______")).count()); + Assertions.assertEquals(40, sc.textFile(workingDir.toString() + "/projectIds").count()); + } + @Test + void testMatchOne() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(11, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(0, tmp.filter(p -> p.getId().substring(3, 15).equals("corda__h2020")).count()); + Assertions.assertEquals(39, sc.textFile(workingDir.toString() + "/projectIds").count()); + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects new file mode 100644 index 000000000..82d9bef76 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects @@ -0,0 +1,12 @@ +{"id":"40|aka_________::01bb7b48e29d732a1c7bc5150b9195c4","websiteurl":null,"code":"135027","acronym":null,"title":"Dynamic 3D resolution-enhanced low-coherence interferometric imaging / Consortium: Hi-Lo","startdate":null,"enddate":null,"callidentifier":"Fotoniikka ja modernit kuvantamismenetelmät LT","keywords":null,"openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","funding_stream":null}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|aka_________::9d1af21dbd0f5bc719f71553d19a6b3a","websiteurl":null,"code":"316061","acronym":null,"title":"Finnish Imaging of Degenerative Shoulder Study (FIMAGE): A study on the prevalence of degenerative imaging changes of the shoulder and their relevance to clinical symptoms in the general population.","startdate":null,"enddate":null,"callidentifier":"Academy Project Funding TT","keywords":null,"openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"AKA","name":"Academy of Finland","jurisdiction":"FI","funding_stream":null}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|anr_________::1f21edc5c902be305ee47148955c6e50","websiteurl":null,"code":"ANR-17-CE05-0033","acronym":"MOISE","title":"METAL OXIDES AS LOW LOADED NANO-IRIDIUM SUPPORT FOR COMPETITIVE WATER 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+{"id":"40|arc_________::838e781a8d479e27a11101421fd8b296","websiteurl":"http://purl.org/au-research/grants/arc/LE0347462","code":"LE0347462","acronym":null,"title":"Femtosecond laser micromachining facility","startdate":"2003-01-01","enddate":"2003-12-31","callidentifier":null,"keywords":"biomedical nanostructures,femtosecond laser machining,laser manufacturing,laser micromachining,microphotonics,photonic bandgap structures","openaccessmandateforpublications":false,"openaccessmandatefordataset":false,"subject":[],"funding":[{"shortName":"ARC","name":"Australian Research Council (ARC)","jurisdiction":"AU","funding_stream":{"id":"ARC::Linkage Infrastructure, Equipment and Facilities","description":"Linkage Infrastructure, Equipment and Facilities"}}],"summary":null,"granted":null,"h2020programme":[]} +{"id":"40|arc_________::a461f180f7b6700c0499d4d3d53e58c7","websiteurl":"http://purl.org/au-research/grants/arc/LP140100567","code":"LP140100567","acronym":null,"title":"Linkage Projects - 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