From 6f8720982c7f994f8dd86d1b9a905bae298d7146 Mon Sep 17 00:00:00 2001 From: miconis Date: Fri, 9 Oct 2020 09:30:23 +0200 Subject: [PATCH] bug fix in the idgenerator and test implementation --- .../dhp/oa/dedup/DedupRecordFactory.java | 1 - .../eu/dnetlib/dhp/oa/dedup/IdGenerator.java | 32 ++-- .../dhp/oa/dedup/model/Identifier.java | 2 +- .../dnetlib/dhp/oa/dedup/IdGeneratorTest.java | 140 ++++++++++++++++++ .../dedup/json/publication_idgeneration.json | 3 + 5 files changed, 165 insertions(+), 13 deletions(-) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/IdGeneratorTest.java create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_idgeneration.json diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index d488f4340..2e4b219b5 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -1,4 +1,3 @@ - package eu.dnetlib.dhp.oa.dedup; import java.util.*; diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java index 2831ab5d0..7980d8e69 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java @@ -24,6 +24,7 @@ public class IdGenerator implements Serializable { public static String CROSSREF_ID = "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2"; public static String DATACITE_ID = "10|openaire____::9e3be59865b2c1c335d32dae2fe7b254"; + public static String BASE_DATE = "2000-01-01"; // pick the best pid from the list (consider date and pidtype) public static String generate(List pids, String defaultID) { @@ -45,14 +46,27 @@ public class IdGenerator implements Serializable { } + public static ArrayList createBasePid(T entity, SimpleDateFormat sdf) { + + Date date; + try { + date = sdf.parse(BASE_DATE); + } catch (ParseException e) { + date = new Date(); + } + return Lists + .newArrayList( + new Identifier(new StructuredProperty(), date, PidType.original, entity.getCollectedfrom(), + EntityType.fromClass(entity.getClass()), entity.getId())); + } + // pick the best pid from the entity. Returns a list (length 1) to save time in the call public static List bestPidToIdentifier(T entity) { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + if (entity.getPid() == null || entity.getPid().size() == 0) - return Lists - .newArrayList( - new Identifier(new StructuredProperty(), new Date(), PidType.original, entity.getCollectedfrom(), - EntityType.fromClass(entity.getClass()), entity.getId())); + return createBasePid(entity, sdf); Optional bp = entity .getPid() @@ -64,14 +78,10 @@ public class IdGenerator implements Serializable { .map( structuredProperty -> Lists .newArrayList( - new Identifier(structuredProperty, extractDate(entity, new SimpleDateFormat("yyyy-MM-dd")), + new Identifier(structuredProperty, extractDate(entity, sdf), PidType.classidValueOf(structuredProperty.getQualifier().getClassid()), entity.getCollectedfrom(), EntityType.fromClass(entity.getClass()), entity.getId()))) - .orElseGet( - () -> Lists - .newArrayList( - new Identifier(new StructuredProperty(), new Date(), PidType.original, - entity.getCollectedfrom(), EntityType.fromClass(entity.getClass()), entity.getId()))); + .orElseGet(() -> createBasePid(entity, sdf)); } @@ -91,7 +101,7 @@ public class IdGenerator implements Serializable { // 00-01-01 public static Date extractDate(T duplicate, SimpleDateFormat sdf) { - String date = "2000-01-01"; + String date = BASE_DATE; if (ModelSupport.isSubClass(duplicate, Result.class)) { Result result = (Result) duplicate; if (isWellformed(result.getDateofacceptance())) { diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java index 30b1582f7..95fd21c64 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java @@ -118,7 +118,7 @@ public class Identifier implements Serializable, Comparable { if (this.getDate().compareTo(i.getDate()) == 0) {// same date - if (this.originalID.compareTo(i.originalID) > 0) + if (this.originalID.compareTo(i.originalID) < 0) this.useOriginal = true; else i.setUseOriginal(true); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/IdGeneratorTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/IdGeneratorTest.java new file mode 100644 index 000000000..1bf851527 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/IdGeneratorTest.java @@ -0,0 +1,140 @@ +package eu.dnetlib.dhp.oa.dedup; + +import com.google.common.collect.Lists; +import eu.dnetlib.dhp.oa.dedup.model.Identifier; +import eu.dnetlib.dhp.oa.dedup.model.PidType; +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.pace.util.MapDocumentUtil; +import org.codehaus.jackson.map.ObjectMapper; +import org.junit.jupiter.api.*; +import scala.Tuple2; +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.BufferedReader; +import java.io.FileReader; +import java.io.IOException; +import java.nio.file.Paths; +import java.text.SimpleDateFormat; +import java.util.ArrayList; +import java.util.Date; +import java.util.List; + +@TestMethodOrder(MethodOrderer.OrderAnnotation.class) +public class IdGeneratorTest { + + private static List bestIds; + private static List> pubs; + + private static List bestIds2; + private static List bestIds3; + + private static String testEntityBasePath; + + private static SimpleDateFormat sdf; + private static Date baseDate; + + @BeforeAll + public static void setUp() throws Exception { + + sdf = new SimpleDateFormat("yyyy-MM-dd"); + baseDate = sdf.parse("2000-01-01"); + + bestIds = new ArrayList<>(); + bestIds2 = Lists.newArrayList( + new Identifier(pid("pid1", "original", "original"), baseDate, PidType.original, keyValue("key", "value"), EntityType.publication, "50|originalID1"), + new Identifier(pid("pid2", "original", "original"), baseDate, PidType.original, keyValue("key", "value"), EntityType.publication, "50|originalID2"), + new Identifier(pid("pid3", "original", "original"), baseDate, PidType.original, keyValue("key", "value"), EntityType.publication, "50|originalID3") + ); + bestIds3 = Lists.newArrayList( + new Identifier(pid("pid1", "original", "original"), baseDate, PidType.original, keyValue("key", "value"), EntityType.publication, "50|originalID1"), + new Identifier(pid("pid2", "doi", "doi"), baseDate, PidType.doi, keyValue("key", "value"), EntityType.publication, "50|originalID2"), + new Identifier(pid("pid3", "original", "original"), baseDate, PidType.original, keyValue("key", "value"), EntityType.publication, "50|originalID3") + ); + + testEntityBasePath = Paths + .get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/json").toURI()) + .toFile() + .getAbsolutePath(); + + pubs = readSample(testEntityBasePath + "/publication_idgeneration.json", Publication.class); + + } + + @Test + @Order(1) + public void bestPidToIdentifierTest(){ + + List typesForAssertions = Lists.newArrayList(PidType.pmc.toString(), PidType.doi.toString(), PidType.doi.toString()); + + for (Tuple2 pub : pubs) { + List ids = IdGenerator.bestPidToIdentifier(pub._2()); + assertEquals(typesForAssertions.get(pubs.indexOf(pub)), ids.get(0).getPid().getQualifier().getClassid()); + bestIds.addAll(ids); + } + } + + @Test + @Order(2) + public void generateIdTest1(){ + String id1 = IdGenerator.generate(bestIds, "50|defaultID"); + + assertEquals("50|dedup_doi___::84f2cc49e3af11f20952eae15cdae066", id1); + } + + @Test + public void generateIdTest2(){ + String id1 = IdGenerator.generate(bestIds2, "50|defaultID"); + String id2 = IdGenerator.generate(bestIds3, "50|defaultID"); + + assertEquals("50|dedup_wf_001::2c56cc1914bffdb30fdff354e0099612", id1); + assertEquals("50|dedup_doi___::128ead3ed8d9ecf262704b6fcf592b8d", id2); + } + + public static List> readSample(String path, Class clazz) { + List> res = new ArrayList<>(); + BufferedReader reader; + try { + reader = new BufferedReader(new FileReader(path)); + String line = reader.readLine(); + while (line != null) { + res + .add( + new Tuple2<>( + MapDocumentUtil.getJPathString("$.id", line), + new ObjectMapper().readValue(line, clazz))); + // read next line + line = reader.readLine(); + } + reader.close(); + } catch (IOException e) { + e.printStackTrace(); + } + + return res; + } + + public static StructuredProperty pid(String pid, String classid, String classname){ + + StructuredProperty sp = new StructuredProperty(); + sp.setValue(pid); + Qualifier q = new Qualifier(); + q.setSchemeid(classid); + q.setSchemename(classname); + q.setClassname(classname); + q.setClassid(classid); + sp.setQualifier(q); + return sp; + } + + public static List keyValue(String key, String value){ + + KeyValue kv = new KeyValue(); + kv.setKey(key); + kv.setValue(value); + return Lists.newArrayList(kv); + } +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_idgeneration.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_idgeneration.json new file mode 100644 index 000000000..b2300acc6 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_idgeneration.json @@ -0,0 +1,3 @@ +{"context": [], "dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk:datasetarchive", "classname": "sysimport:crosswalk:datasetarchive", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "dedup-similarity-result-levenstein", 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