From 110ce4b40fc54c2d60fe8120927e76b84580b8c9 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 10 Oct 2023 09:46:40 +0200 Subject: [PATCH 1/2] extend the fos model to include the level4 and the scores for level3 and level4. removed bip indicators from the instance --- .../dnetlib/dhp/actionmanager/Constants.java | 20 ++++-- .../GetFOSSparkJob.java | 9 ++- .../PrepareFOSSparkJob.java | 27 +++++-- .../SparkSaveUnresolved.java | 6 +- .../model/FOSDataModel.java | 63 +++++++++++++++-- .../CreateActionSetSparkJob.java | 2 +- .../oozie_app/workflow.xml | 56 +++++++-------- .../createunresolvedentities/GetFosTest.java | 39 +++++++++-- .../createunresolvedentities/PrepareTest.java | 70 +++++++++++++++++++ .../createunresolvedentities/ProduceTest.java | 34 +++++++++ .../createunresolvedentities/fos/fos_sbs2.csv | 26 +++++++ .../fos/fos_sbs_2.json | 25 +++++++ .../doiboost/crossref/Crossref2Oaf.scala | 16 +++-- .../crossref/CrossrefMappingTest.scala | 2 +- 14 files changed, 334 insertions(+), 61 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs2.csv create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs_2.json diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java index 62556b16b..006d3af76 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java @@ -40,6 +40,7 @@ public class Constants { public static final String SDG_CLASS_NAME = "Sustainable Development Goals"; public static final String NULL = "NULL"; + public static final String NA = "N/A"; public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); @@ -61,10 +62,16 @@ public class Constants { .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); } - public static Subject getSubject(String sbj, String classid, String classname, - String diqualifierclassid) { - if (sbj == null || sbj.equals(NULL)) + public static Subject getSubject(String sbj, String classid, String classname, String diqualifierclassid, + Boolean split) { + if (sbj == null || sbj.equals(NULL) || sbj.startsWith(NA)) return null; + String trust = ""; + String subject = sbj; + if (split) { + sbj = subject.split("@@")[0]; + trust = subject.split("@@")[1]; + } Subject s = new Subject(); s.setValue(sbj); s @@ -89,9 +96,14 @@ public class Constants { UPDATE_CLASS_NAME, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), - "")); + trust)); return s; + } + + public static Subject getSubject(String sbj, String classid, String classname, + String diqualifierclassid) { + return getSubject(sbj, classid, classname, diqualifierclassid, false); } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSSparkJob.java index 0cc2f93df..abea6acd7 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSSparkJob.java @@ -75,9 +75,12 @@ public class GetFOSSparkJob implements Serializable { fosData.map((MapFunction) r -> { FOSDataModel fosDataModel = new FOSDataModel(); fosDataModel.setDoi(r.getString(0).toLowerCase()); - fosDataModel.setLevel1(r.getString(1)); - fosDataModel.setLevel2(r.getString(2)); - fosDataModel.setLevel3(r.getString(3)); + fosDataModel.setLevel1(r.getString(2)); + fosDataModel.setLevel2(r.getString(3)); + fosDataModel.setLevel3(r.getString(4)); + fosDataModel.setLevel4(r.getString(5)); + fosDataModel.setScoreL3(String.valueOf(r.getDouble(6))); + fosDataModel.setScoreL4(String.valueOf(r.getDouble(7))); return fosDataModel; }, Encoders.bean(FOSDataModel.class)) .write() diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java index 4d2d25215..57ad8b96a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java @@ -78,12 +78,20 @@ public class PrepareFOSSparkJob implements Serializable { HashSet level1 = new HashSet<>(); HashSet level2 = new HashSet<>(); HashSet level3 = new HashSet<>(); - addLevels(level1, level2, level3, first); - it.forEachRemaining(v -> addLevels(level1, level2, level3, v)); + HashSet level4 = new HashSet<>(); + addLevels(level1, level2, level3, level4, first); + it.forEachRemaining(v -> addLevels(level1, level2, level3, level4, v)); List sbjs = new ArrayList<>(); - level1.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID))); - level2.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID))); - level3.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID))); + level1 + .forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID))); + level2 + .forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID))); + level3 + .forEach( + l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true))); + level4 + .forEach( + l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true))); r.setSubject(sbjs); r .setDataInfo( @@ -106,11 +114,18 @@ public class PrepareFOSSparkJob implements Serializable { .json(outputPath + "/fos"); } + private static void add(List sbsjs, Subject sbj) { + if (sbj != null) + sbsjs.add(sbj); + } + private static void addLevels(HashSet level1, HashSet level2, HashSet level3, + HashSet level4, FOSDataModel first) { level1.add(first.getLevel1()); level2.add(first.getLevel2()); - level3.add(first.getLevel3()); + level3.add(first.getLevel3() + "@@" + first.getScoreL3()); + level4.add(first.getLevel4() + "@@" + first.getScoreL4()); } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/SparkSaveUnresolved.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/SparkSaveUnresolved.java index 3b9775094..93bbfcc88 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/SparkSaveUnresolved.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/SparkSaveUnresolved.java @@ -69,9 +69,9 @@ public class SparkSaveUnresolved implements Serializable { .mapGroups((MapGroupsFunction) (k, it) -> { Result ret = it.next(); it.forEachRemaining(r -> { - if (r.getInstance() != null) { - ret.setInstance(r.getInstance()); - } +// if (r.getInstance() != null) { +// ret.setInstance(r.getInstance()); +// } if (r.getSubject() != null) { if (ret.getSubject() != null) ret.getSubject().addAll(r.getSubject()); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/FOSDataModel.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/FOSDataModel.java index e98ba74a1..a82d7bfd6 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/FOSDataModel.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/FOSDataModel.java @@ -11,21 +11,43 @@ public class FOSDataModel implements Serializable { private String doi; @CsvBindByPosition(position = 1) +// @CsvBindByName(column = "doi") + private String oaid; + @CsvBindByPosition(position = 2) // @CsvBindByName(column = "level1") private String level1; - @CsvBindByPosition(position = 2) + @CsvBindByPosition(position = 3) // @CsvBindByName(column = "level2") private String level2; - @CsvBindByPosition(position = 3) + @CsvBindByPosition(position = 4) // @CsvBindByName(column = "level3") private String level3; + @CsvBindByPosition(position = 5) +// @CsvBindByName(column = "level3") + private String level4; + @CsvBindByPosition(position = 6) + private String scoreL3; + @CsvBindByPosition(position = 7) + private String scoreL4; + public FOSDataModel() { } + public FOSDataModel(String doi, String level1, String level2, String level3, String level4, String l3score, + String l4score) { + this.doi = doi; + this.level1 = level1; + this.level2 = level2; + this.level3 = level3; + this.level4 = level4; + this.scoreL3 = l3score; + this.scoreL4 = l4score; + } + public FOSDataModel(String doi, String level1, String level2, String level3) { this.doi = doi; this.level1 = level1; @@ -33,8 +55,41 @@ public class FOSDataModel implements Serializable { this.level3 = level3; } - public static FOSDataModel newInstance(String d, String level1, String level2, String level3) { - return new FOSDataModel(d, level1, level2, level3); + public static FOSDataModel newInstance(String d, String level1, String level2, String level3, String level4, + String scorel3, String scorel4) { + return new FOSDataModel(d, level1, level2, level3, level4, scorel3, scorel4); + } + + public String getOaid() { + return oaid; + } + + public void setOaid(String oaid) { + this.oaid = oaid; + } + + public String getLevel4() { + return level4; + } + + public void setLevel4(String level4) { + this.level4 = level4; + } + + public String getScoreL3() { + return scoreL3; + } + + public void setScoreL3(String scoreL3) { + this.scoreL3 = scoreL3; + } + + public String getScoreL4() { + return scoreL4; + } + + public void setScoreL4(String scoreL4) { + this.scoreL4 = scoreL4; } public String getDoi() { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java index a367ba852..b707fdcd3 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java @@ -7,7 +7,6 @@ import java.io.IOException; import java.io.Serializable; import java.util.*; -import eu.dnetlib.dhp.schema.oaf.utils.*; import org.apache.commons.cli.ParseException; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; @@ -30,6 +29,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.*; import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml index c8af64594..a2935a71d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml @@ -6,10 +6,10 @@ the input path of the resources to be extended - - bipScorePath - the path where to find the bipFinder scores - + + + + outputPath the path where to store the actionset @@ -77,34 +77,34 @@ - + - - - yarn - cluster - Produces the unresolved from BIP! Finder - eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareBipFinder - dhp-aggregation-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${bipScorePath} - --outputPath${workingDir}/prepared - - - - + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFosTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFosTest.java index 7e0acc2bb..d4fe129df 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFosTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFosTest.java @@ -13,10 +13,7 @@ import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; 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.junit.jupiter.api.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -68,6 +65,7 @@ public class GetFosTest { } @Test + @Disabled void test3() throws Exception { final String sourcePath = getClass() .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs.tsv") @@ -96,4 +94,37 @@ public class GetFosTest { tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null)); } + + @Test + void test4() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs2.csv") + .getPath(); + + final String outputPath = workingDir.toString() + "/fos.json"; + GetFOSSparkJob + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", sourcePath, + "--delimiter", ",", + "-outputPath", outputPath + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(outputPath) + .map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class)); + + tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null)); + tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null)); + tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null)); + tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null)); + tmp.foreach(t -> Assertions.assertTrue(t.getLevel4() != null)); + tmp.foreach(t -> Assertions.assertTrue(t.getScoreL3() != null)); + tmp.foreach(t -> Assertions.assertTrue(t.getScoreL4() != null)); + + } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java index cc8108bde..ccb0ebbff 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java @@ -222,6 +222,76 @@ public class PrepareTest { } + @Test + void fosPrepareTest2() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs_2.json") + .getPath(); + + PrepareFOSSparkJob + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", sourcePath, + + "-outputPath", workingDir.toString() + "/work" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/work/fos") + .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + + String doi1 = "unresolved::10.1016/j.revmed.2006.07.012::doi"; + + assertEquals(13, tmp.count()); + assertEquals(1, tmp.filter(row -> row.getId().equals(doi1)).count()); + + Result result = tmp + .filter(r -> r.getId().equals(doi1)) + .first(); + + result.getSubject().forEach(s -> System.out.println(s.getValue() + " trust = " + s.getDataInfo().getTrust())); + Assertions.assertEquals(6, result.getSubject().size()); + + assertTrue( + result + .getSubject() + .stream() + .anyMatch( + s -> s.getValue().contains("03 medical and health sciences") + && s.getDataInfo().getTrust().equals(""))); + + assertTrue( + result + .getSubject() + .stream() + .anyMatch( + s -> s.getValue().contains("0302 clinical medicine") && s.getDataInfo().getTrust().equals(""))); + + assertTrue( + result + .getSubject() + .stream() + .anyMatch( + s -> s + .getValue() + .contains("030204 cardiovascular system & hematology") + && s.getDataInfo().getTrust().equals("0.5101401805877686"))); + assertTrue( + result + .getSubject() + .stream() + .anyMatch( + s -> s + .getValue() + .contains("03020409 Hematology/Coagulopathies") + && s.getDataInfo().getTrust().equals("0.0546871414174914"))); + + } + @Test void sdgPrepareTest() throws Exception { final String sourcePath = getClass() diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java index c3c110f09..fce6c1e97 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java @@ -379,6 +379,40 @@ public class ProduceTest { .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); } + @Test + public JavaRDD getResultFosJavaRDD() throws Exception { + + final String fosPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs_2.json") + .getPath(); + + PrepareFOSSparkJob + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", fosPath, + "-outputPath", workingDir.toString() + "/work" + }); + + SparkSaveUnresolved.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", workingDir.toString() + "/work", + + "-outputPath", workingDir.toString() + "/unresolved" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/unresolved") + .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + + return tmp; + + } + @Test void prepareTest5Subjects() throws Exception { final String doi = "unresolved::10.1063/5.0032658::doi"; diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs2.csv b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs2.csv new file mode 100644 index 000000000..3b1f2304f --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs2.csv @@ -0,0 +1,26 @@ +DOI,OAID,level1,level2,level3,level4,score_for_L3,score_for_L4 +10.1016/j.anucene.2006.02.004,doi_________::00059d9963edf633bec756fb21b5bd72,02 engineering and technology,"0202 electrical engineering, electronic engineering, information engineering",020209 energy,02020908 Climate change policy/Ethanol fuel,0.5,0.5 +10.1016/j.anucene.2006.02.004,doi_________::00059d9963edf633bec756fb21b5bd72,02 engineering and technology,0211 other engineering and technologies,021108 energy,02110808 Climate change policy/Ethanol fuel,0.5,0.5 +10.1016/j.revmed.2006.07.010,doi_________::0026476c1651a92c933d752ff12496c7,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis,N/A,0.5036656856536865,0.0 +10.1016/j.revmed.2006.07.010,doi_________::0026476c1651a92c933d752ff12496c7,03 medical and health sciences,0302 clinical medicine,030212 general & internal medicine,N/A,0.4963343143463135,0.0 +10.20965/jrm.2006.p0312,doi_________::0028336a2f3826cc83c47dbefac71543,02 engineering and technology,0209 industrial biotechnology,020901 industrial engineering & automation,02090104 Robotics/Robots,0.6111094951629639,0.5053805979936855 +10.20965/jrm.2006.p0312,doi_________::0028336a2f3826cc83c47dbefac71543,01 natural sciences,0104 chemical sciences,010401 analytical chemistry,N/A,0.3888905048370361,0.0 +10.1111/j.1747-7379.2006.040_1.x,doi_________::002c7077e7c114a8304eb90f59e45fa4,05 social sciences,0506 political science,050602 political science & public administration,05060202 Ethnic groups/Ethnicity,0.6159052848815918,0.7369035568037298 +10.1111/j.1747-7379.2006.040_1.x,doi_________::002c7077e7c114a8304eb90f59e45fa4,05 social sciences,0502 economics and business,050207 economics,N/A,0.3840946555137634,0.0 +10.1007/s10512-006-0049-9,doi_________::003f29f9254819cf4c78558b1bc25f10,02 engineering and technology,"0202 electrical engineering, electronic engineering, information engineering",020209 energy,02020908 Climate change policy/Ethanol fuel,0.5,0.5 +10.1007/s10512-006-0049-9,doi_________::003f29f9254819cf4c78558b1bc25f10,02 engineering and technology,0211 other engineering and technologies,021108 energy,02110808 Climate change policy/Ethanol fuel,0.5,0.5 +10.1111/j.1365-2621.2005.01045.x,doi_________::00419355b4c3e0646bd0e1b301164c8e,04 agricultural and veterinary sciences,0404 agricultural biotechnology,040401 food science,04040102 Food science/Food industry,0.5,0.5 +10.1111/j.1365-2621.2005.01045.x,doi_________::00419355b4c3e0646bd0e1b301164c8e,04 agricultural and veterinary sciences,0405 other agricultural sciences,040502 food science,04050202 Food science/Food industry,0.5,0.5 +10.1002/chin.200617262,doi_________::004c8cef80668904961b9e62841793c8,01 natural sciences,0104 chemical sciences,010405 organic chemistry,01040508 Functional groups/Ethers,0.5566747188568115,0.5582916736602783 +10.1002/chin.200617262,doi_________::004c8cef80668904961b9e62841793c8,01 natural sciences,0104 chemical sciences,010402 general chemistry,01040207 Chemical synthesis/Total synthesis,0.4433253407478332,0.4417082965373993 +10.1016/j.revmed.2006.07.012,doi_________::005b1d0fb650b680abaf6cfe26a21604,03 medical and health sciences,0302 clinical medicine,030204 cardiovascular system & hematology,03020409 Hematology/Coagulopathies,0.5101401805877686,0.0546871414174914 +10.1016/j.revmed.2006.07.012,doi_________::005b1d0fb650b680abaf6cfe26a21604,03 medical and health sciences,0301 basic medicine,030105 genetics & heredity,N/A,0.4898599088191986,0.0 +10.4109/jslab.17.132,doi_________::00889baa06de363e37930daaf8e800c0,03 medical and health sciences,0301 basic medicine,030104 developmental biology,N/A,0.5,0.0 +10.4109/jslab.17.132,doi_________::00889baa06de363e37930daaf8e800c0,03 medical and health sciences,0303 health sciences,030304 developmental biology,N/A,0.5,0.0 +10.1108/00251740610715687,doi_________::0092cb1b1920d556719385a26363ecaa,05 social sciences,0502 economics and business,050203 business & management,05020311 International business/International trade,0.605047881603241,0.2156608108845153 +10.1108/00251740610715687,doi_________::0092cb1b1920d556719385a26363ecaa,05 social sciences,0502 economics and business,050211 marketing,N/A,0.394952118396759,0.0 +10.1080/03067310500248098,doi_________::00a76678d230e3f20b6356804448028f,04 agricultural and veterinary sciences,0404 agricultural biotechnology,040401 food science,04040102 Food science/Food industry,0.5,0.5 +10.1080/03067310500248098,doi_________::00a76678d230e3f20b6356804448028f,04 agricultural and veterinary sciences,0405 other agricultural sciences,040502 food science,04050202 Food science/Food industry,0.5,0.5 +10.3152/147154306781778533,doi_________::00acc520f3939e5a6675343881fed4f2,05 social sciences,0502 economics and business,050203 business & management,05020307 Innovation/Product management,0.5293408632278442,0.5326762795448303 +10.3152/147154306781778533,doi_________::00acc520f3939e5a6675343881fed4f2,05 social sciences,0509 other social sciences,050905 science studies,05090502 Social philosophy/Capitalism,0.4706590473651886,0.4673237204551697 +10.1785/0120050806,doi_________::00d5831d329e7ae4523d78bfc3042e98,02 engineering and technology,0211 other engineering and technologies,021101 geological & geomatics engineering,02110103 Concrete/Building materials,0.5343400835990906,0.3285667930180677 \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs_2.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs_2.json new file mode 100644 index 000000000..00ffad70c --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs_2.json @@ -0,0 +1,25 @@ +{"doi":"10.1016/j.anucene.2006.02.004","level1":"02 engineering and technology","level2":"0202 electrical engineering, electronic engineering, information engineering","level3":"020209 energy","level4":"02020908 Climate change policy/Ethanol fuel","scoreL3":"0.5","scoreL4":"0.5"} +{"doi":"10.1016/j.anucene.2006.02.004","level1":"02 engineering and technology","level2":"0211 other engineering and technologies","level3":"021108 energy","level4":"02110808 Climate change policy/Ethanol fuel","scoreL3":"0.5","scoreL4":"0.5"} +{"doi":"10.1016/j.revmed.2006.07.010","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030220 oncology & carcinogenesis","level4":"N/A","scoreL3":"0.5036656856536865","scoreL4":"0.0"} +{"doi":"10.1016/j.revmed.2006.07.010","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030212 general & internal medicine","level4":"N/A","scoreL3":"0.4963343143463135","scoreL4":"0.0"} +{"doi":"10.20965/jrm.2006.p0312","level1":"02 engineering and technology","level2":"0209 industrial biotechnology","level3":"020901 industrial engineering & automation","level4":"02090104 Robotics/Robots","scoreL3":"0.6111094951629639","scoreL4":"0.5053805979936855"} +{"doi":"10.20965/jrm.2006.p0312","level1":"01 natural sciences","level2":"0104 chemical sciences","level3":"010401 analytical chemistry","level4":"N/A","scoreL3":"0.3888905048370361","scoreL4":"0.0"} +{"doi":"10.1111/j.1747-7379.2006.040_1.x","level1":"05 social sciences","level2":"0506 political science","level3":"050602 political science & public administration","level4":"05060202 Ethnic groups/Ethnicity","scoreL3":"0.6159052848815918","scoreL4":"0.7369035568037298"} +{"doi":"10.1111/j.1747-7379.2006.040_1.x","level1":"05 social sciences","level2":"0502 economics and business","level3":"050207 economics","level4":"N/A","scoreL3":"0.3840946555137634","scoreL4":"0.0"} +{"doi":"10.1007/s10512-006-0049-9","level1":"02 engineering and technology","level2":"0202 electrical engineering, electronic engineering, information engineering","level3":"020209 energy","level4":"02020908 Climate change policy/Ethanol fuel","scoreL3":"0.5","scoreL4":"0.5"} +{"doi":"10.1007/s10512-006-0049-9","level1":"02 engineering and technology","level2":"0211 other engineering and technologies","level3":"021108 energy","level4":"02110808 Climate change policy/Ethanol fuel","scoreL3":"0.5","scoreL4":"0.5"} +{"doi":"10.1111/j.1365-2621.2005.01045.x","level1":"04 agricultural and veterinary sciences","level2":"0404 agricultural biotechnology","level3":"040401 food science","level4":"04040102 Food science/Food industry","scoreL3":"0.5","scoreL4":"0.5"} +{"doi":"10.1111/j.1365-2621.2005.01045.x","level1":"04 agricultural and veterinary sciences","level2":"0405 other agricultural sciences","level3":"040502 food science","level4":"04050202 Food science/Food industry","scoreL3":"0.5","scoreL4":"0.5"} +{"doi":"10.1002/chin.200617262","level1":"01 natural sciences","level2":"0104 chemical sciences","level3":"010405 organic chemistry","level4":"01040508 Functional groups/Ethers","scoreL3":"0.5566747188568115","scoreL4":"0.5582916736602783"} +{"doi":"10.1002/chin.200617262","level1":"01 natural sciences","level2":"0104 chemical sciences","level3":"010402 general chemistry","level4":"01040207 Chemical synthesis/Total synthesis","scoreL3":"0.4433253407478332","scoreL4":"0.4417082965373993"} +{"doi":"10.1016/j.revmed.2006.07.012","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030204 cardiovascular system & hematology","level4":"03020409 Hematology/Coagulopathies","scoreL3":"0.5101401805877686","scoreL4":"0.0546871414174914"} +{"doi":"10.1016/j.revmed.2006.07.012","level1":"03 medical and health sciences","level2":"0301 basic medicine","level3":"030105 genetics & heredity","level4":"N/A","scoreL3":"0.4898599088191986","scoreL4":"0.0"} +{"doi":"10.4109/jslab.17.132","level1":"03 medical and health sciences","level2":"0301 basic medicine","level3":"030104 developmental biology","level4":"N/A","scoreL3":"0.5","scoreL4":"0.0"} +{"doi":"10.4109/jslab.17.132","level1":"03 medical and health sciences","level2":"0303 health sciences","level3":"030304 developmental biology","level4":"N/A","scoreL3":"0.5","scoreL4":"0.0"} +{"doi":"10.1108/00251740610715687","level1":"05 social sciences","level2":"0502 economics and business","level3":"050203 business & management","level4":"05020311 International business/International trade","scoreL3":"0.605047881603241","scoreL4":"0.2156608108845153"} +{"doi":"10.1108/00251740610715687","level1":"05 social sciences","level2":"0502 economics and business","level3":"050211 marketing","level4":"N/A","scoreL3":"0.394952118396759","scoreL4":"0.0"} +{"doi":"10.1080/03067310500248098","level1":"04 agricultural and veterinary sciences","level2":"0404 agricultural biotechnology","level3":"040401 food science","level4":"04040102 Food science/Food industry","scoreL3":"0.5","scoreL4":"0.5"} +{"doi":"10.1080/03067310500248098","level1":"04 agricultural and veterinary sciences","level2":"0405 other agricultural sciences","level3":"040502 food science","level4":"04050202 Food science/Food industry","scoreL3":"0.5","scoreL4":"0.5"} +{"doi":"10.3152/147154306781778533","level1":"05 social sciences","level2":"0502 economics and business","level3":"050203 business & management","level4":"05020307 Innovation/Product management","scoreL3":"0.5293408632278442","scoreL4":"0.5326762795448303"} +{"doi":"10.3152/147154306781778533","level1":"05 social sciences","level2":"0509 other social sciences","level3":"050905 science studies","level4":"05090502 Social philosophy/Capitalism","scoreL3":"0.4706590473651886","scoreL4":"0.4673237204551697"} +{"doi":"10.1785/0120050806","level1":"02 engineering and technology","level2":"0211 other engineering and technologies","level3":"021101 geological & geomatics engineering","level4":"02110103 Concrete/Building materials","scoreL3":"0.5343400835990906","scoreL4":"0.3285667930180677"} diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index e0fdb9ce4..565d34e62 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -31,9 +31,7 @@ case class mappingAuthor( affiliation: Option[mappingAffiliation] ) {} -case class funderInfo(id:String,uri:String, name:String,synonym:List[String] ) {} - - +case class funderInfo(id: String, uri: String, name: String, synonym: List[String]) {} case class mappingFunder(name: String, DOI: Option[String], award: Option[List[String]]) {} @@ -41,7 +39,9 @@ case object Crossref2Oaf { val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass) val irishFunder: List[funderInfo] = { - val s = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref/irish_funder.json")).mkString + val s = Source + .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref/irish_funder.json")) + .mkString implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json: org.json4s.JValue = parse(s) json.extract[List[funderInfo]] @@ -100,9 +100,11 @@ case object Crossref2Oaf { "report" -> "0017 Report" ) - def getIrishId(doi:String):Option[String] = { - val id =doi.split("/").last - irishFunder.find(f => id.equalsIgnoreCase(f.id) || (f.synonym.nonEmpty && f.synonym.exists(s => s.equalsIgnoreCase(id)))).map(f => f.id) + def getIrishId(doi: String): Option[String] = { + val id = doi.split("/").last + irishFunder + .find(f => id.equalsIgnoreCase(f.id) || (f.synonym.nonEmpty && f.synonym.exists(s => s.equalsIgnoreCase(id)))) + .map(f => f.id) } def mappingResult(result: Result, json: JValue, cobjCategory: String): Result = { diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index 7961376c5..fbf6f72c0 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -50,7 +50,7 @@ class CrossrefMappingTest { } } - def checkRelation(generatedOAF: List[Oaf]): Unit = { + def checkRelation(generatedOAF: List[Oaf]): Unit = { val rels: List[Relation] = generatedOAF.filter(p => p.isInstanceOf[Relation]).asInstanceOf[List[Relation]] From a431b04814dc55c56ab2bde7d2a2663b7fc0950a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 10 Oct 2023 12:53:57 +0200 Subject: [PATCH 2/2] leftover for the properties and removal of bipfinder --- .../PrepareBipFinder.java | 178 ------------------ .../oozie_app/workflow.xml | 31 +-- .../createunresolvedentities/PrepareTest.java | 139 -------------- .../createunresolvedentities/ProduceTest.java | 30 --- 4 files changed, 1 insertion(+), 377 deletions(-) delete mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java deleted file mode 100644 index 0507f90e5..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java +++ /dev/null @@ -1,178 +0,0 @@ - -package eu.dnetlib.dhp.actionmanager.createunresolvedentities; - -import static eu.dnetlib.dhp.actionmanager.Constants.*; -import static eu.dnetlib.dhp.actionmanager.Constants.UPDATE_CLASS_NAME; -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -import java.io.Serializable; -import java.util.Arrays; -import java.util.List; -import java.util.Optional; -import java.util.stream.Collectors; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore; -import eu.dnetlib.dhp.actionmanager.bipmodel.score.deserializers.BipResultModel; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Measure; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import eu.dnetlib.dhp.utils.DHPUtils; - -public class PrepareBipFinder implements Serializable { - - private static final Logger log = LoggerFactory.getLogger(PrepareBipFinder.class); - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - public static void main(String[] args) throws Exception { - - String jsonConfiguration = IOUtils - .toString( - PrepareBipFinder.class - .getResourceAsStream( - "/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json")); - - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - final String sourcePath = parser.get("sourcePath"); - log.info("sourcePath {}: ", sourcePath); - - final String outputPath = parser.get("outputPath"); - log.info("outputPath {}: ", outputPath); - - SparkConf conf = new SparkConf(); - - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration()); - prepareResults(spark, sourcePath, outputPath); - }); - } - - private static void prepareResults(SparkSession spark, String inputPath, String outputPath) { - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD bipDeserializeJavaRDD = sc - .textFile(inputPath) - .map(item -> OBJECT_MAPPER.readValue(item, BipResultModel.class)); - - spark - .createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> { - BipScore bs = new BipScore(); - bs.setId(key); - bs.setScoreList(entry.get(key)); - - return bs; - }).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class)) - .map((MapFunction) v -> { - Result r = new Result(); - final String cleanedPid = CleaningFunctions.normalizePidValue(DOI, v.getId()); - - r.setId(DHPUtils.generateUnresolvedIdentifier(v.getId(), DOI)); - Instance inst = new Instance(); - inst.setMeasures(getMeasure(v)); - - inst - .setPid( - Arrays - .asList( - OafMapperUtils - .structuredProperty( - cleanedPid, - OafMapperUtils - .qualifier( - DOI, DOI_CLASSNAME, - ModelConstants.DNET_PID_TYPES, - ModelConstants.DNET_PID_TYPES), - null))); - r.setInstance(Arrays.asList(inst)); - r - .setDataInfo( - OafMapperUtils - .dataInfo( - false, null, true, - false, - OafMapperUtils - .qualifier( - ModelConstants.PROVENANCE_ENRICH, - null, - ModelConstants.DNET_PROVENANCE_ACTIONS, - ModelConstants.DNET_PROVENANCE_ACTIONS), - null)); - return r; - }, Encoders.bean(Result.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/bip"); - } - - private static List getMeasure(BipScore value) { - return value - .getScoreList() - .stream() - .map(score -> { - Measure m = new Measure(); - m.setId(score.getId()); - m - .setUnit( - score - .getUnit() - .stream() - .map(unit -> { - KeyValue kv = new KeyValue(); - kv.setValue(unit.getValue()); - kv.setKey(unit.getKey()); - kv - .setDataInfo( - OafMapperUtils - .dataInfo( - false, - UPDATE_DATA_INFO_TYPE, - true, - false, - OafMapperUtils - .qualifier( - UPDATE_MEASURE_BIP_CLASS_ID, - UPDATE_CLASS_NAME, - ModelConstants.DNET_PROVENANCE_ACTIONS, - ModelConstants.DNET_PROVENANCE_ACTIONS), - "")); - return kv; - }) - .collect(Collectors.toList())); - return m; - }) - .collect(Collectors.toList()); - } -} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml index a2935a71d..a5388f28b 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml @@ -5,11 +5,6 @@ fosPath the input path of the resources to be extended - - - - - outputPath the path where to store the actionset @@ -77,35 +72,10 @@ - - - - - - - - - - - - - - - - - - - - - - - - - yarn @@ -125,6 +95,7 @@ --sourcePath${fosPath} --outputPath${workingDir}/input/fos + --delimiter${delimiter} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java index ccb0ebbff..da7bcd3de 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java @@ -67,92 +67,6 @@ public class PrepareTest { spark.stop(); } - @Test - void bipPrepareTest() throws Exception { - final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json") - .getPath(); - - PrepareBipFinder - .main( - new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--sourcePath", sourcePath, - "--outputPath", workingDir.toString() + "/work" - - }); - - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - - JavaRDD tmp = sc - .textFile(workingDir.toString() + "/work/bip") - .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); - - Assertions.assertEquals(86, tmp.count()); - - String doi1 = "unresolved::10.0000/096020199389707::doi"; - - Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).count()); - Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getInstance().size()); - Assertions - .assertEquals( - 3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getInstance().get(0).getMeasures().size()); - Assertions - .assertEquals( - "6.34596412687e-09", tmp - .filter(r -> r.getId().equals(doi1)) - .collect() - .get(0) - .getInstance() - .get(0) - .getMeasures() - .stream() - .filter(sl -> sl.getId().equals("influence")) - .collect(Collectors.toList()) - .get(0) - .getUnit() - .get(0) - .getValue()); - Assertions - .assertEquals( - "0.641151896994", tmp - .filter(r -> r.getId().equals(doi1)) - .collect() - .get(0) - .getInstance() - .get(0) - .getMeasures() - .stream() - .filter(sl -> sl.getId().equals("popularity_alt")) - .collect(Collectors.toList()) - .get(0) - .getUnit() - .get(0) - .getValue()); - Assertions - .assertEquals( - "2.33375102921e-09", tmp - .filter(r -> r.getId().equals(doi1)) - .collect() - .get(0) - .getInstance() - .get(0) - .getMeasures() - .stream() - .filter(sl -> sl.getId().equals("popularity")) - .collect(Collectors.toList()) - .get(0) - .getUnit() - .get(0) - .getValue()); - - final String doi2 = "unresolved::10.3390/s18072310::doi"; - - Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).count()); - Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).collect().get(0).getInstance().size()); - - } - @Test void fosPrepareTest() throws Exception { final String sourcePath = getClass() @@ -338,57 +252,4 @@ public class PrepareTest { } -// @Test -// void test3() throws Exception { -// final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_fos_results_20_12_2021.csv.gz"; -// -// final String outputPath = workingDir.toString() + "/fos.json"; -// GetFOSSparkJob -// .main( -// new String[] { -// "--isSparkSessionManaged", Boolean.FALSE.toString(), -// "--sourcePath", sourcePath, -// -// "-outputPath", outputPath -// -// }); -// -// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); -// -// JavaRDD tmp = sc -// .textFile(outputPath) -// .map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class)); -// -// tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null)); -// tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null)); -// tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null)); -// tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null)); -// -// } -// -// @Test -// void test4() throws Exception { -// final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_sdg_results_20_12_21.csv.gz"; -// -// final String outputPath = workingDir.toString() + "/sdg.json"; -// GetSDGSparkJob -// .main( -// new String[] { -// "--isSparkSessionManaged", Boolean.FALSE.toString(), -// "--sourcePath", sourcePath, -// -// "-outputPath", outputPath -// -// }); -// -// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); -// -// JavaRDD tmp = sc -// .textFile(outputPath) -// .map(item -> OBJECT_MAPPER.readValue(item, SDGDataModel.class)); -// -// tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null)); -// tmp.foreach(t -> Assertions.assertTrue(t.getSbj() != null)); -// -// } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java index fce6c1e97..ce116688a 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java @@ -340,18 +340,7 @@ public class ProduceTest { } private JavaRDD getResultJavaRDD() throws Exception { - final String bipPath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json") - .getPath(); - PrepareBipFinder - .main( - new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--sourcePath", bipPath, - "--outputPath", workingDir.toString() + "/work" - - }); final String fosPath = getClass() .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json") .getPath(); @@ -449,18 +438,7 @@ public class ProduceTest { } private JavaRDD getResultJavaRDDPlusSDG() throws Exception { - final String bipPath = getClass() - .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json") - .getPath(); - PrepareBipFinder - .main( - new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--sourcePath", bipPath, - "--outputPath", workingDir.toString() + "/work" - - }); final String fosPath = getClass() .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json") .getPath(); @@ -517,14 +495,6 @@ public class ProduceTest { .filter(row -> row.getSubject() != null) .count()); - Assertions - .assertEquals( - 85, - tmp - .filter(row -> !row.getId().equals(doi)) - .filter(r -> r.getInstance() != null && r.getInstance().size() > 0) - .count()); - } @Test