From 4dcd03b78ee57c2769e7de0ccb3d63ba042dd8c4 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Sat, 31 Dec 2022 13:00:00 +0100 Subject: [PATCH] minor and fixed wronf number is test because of change in the input resource --- .../src/test/java/GenerateJsonSchema.java | 2 +- .../community/SparkUpdateProjectInfo.java | 8 ++--- .../funderresults/SparkDumpFunderResults.java | 5 ++- .../SparkResultLinkedToProject.java | 13 +++++-- .../graph/dump/wf/main/oozie_app/workflow.xml | 34 +++++++++---------- .../oa/graph/dump/subset/DumpSubsetTest.java | 12 ++++--- .../addProjectInfo/publication_extendedmodel | 8 ++--- 7 files changed, 46 insertions(+), 36 deletions(-) diff --git a/dump-schema/src/test/java/GenerateJsonSchema.java b/dump-schema/src/test/java/GenerateJsonSchema.java index d059db7..1dd03f8 100644 --- a/dump-schema/src/test/java/GenerateJsonSchema.java +++ b/dump-schema/src/test/java/GenerateJsonSchema.java @@ -1,6 +1,5 @@ import java.io.IOException; -import eu.dnetlib.dhp.oa.model.community.CommunityResult; import org.junit.jupiter.api.Test; import com.fasterxml.jackson.core.JsonProcessingException; @@ -10,6 +9,7 @@ import com.github.imifou.jsonschema.module.addon.AddonModule; import com.github.victools.jsonschema.generator.*; import eu.dnetlib.dhp.ExecCreateSchemas; +import eu.dnetlib.dhp.oa.model.community.CommunityResult; import eu.dnetlib.dhp.oa.model.graph.Datasource; import eu.dnetlib.dhp.oa.model.graph.GraphResult; import eu.dnetlib.dhp.oa.model.graph.Organization; diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java index fef3359..996b4e2 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java @@ -8,6 +8,7 @@ import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -71,7 +72,8 @@ public class SparkUpdateProjectInfo implements Serializable { String preparedInfoPath) { Dataset result = Utils.readPath(spark, inputPath, CommunityResult.class); Dataset resultProject = Utils.readPath(spark, preparedInfoPath, ResultProject.class); - Dataset tmp = result + + result .joinWith( resultProject, result.col("id").equalTo(resultProject.col("resultId")), "left") @@ -79,9 +81,7 @@ public class SparkUpdateProjectInfo implements Serializable { CommunityResult r = value._1(); Optional.ofNullable(value._2()).ifPresent(rp -> r.setProjects(rp.getProjectsList())); return r; - }, Encoders.bean(CommunityResult.class)); - long count = tmp.count(); - tmp + }, Encoders.bean(CommunityResult.class)) .map( (MapFunction) cr -> new ObjectMapper().writeValueAsString(cr), Encoders.STRING()) diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index a5b9575..41e3f15 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -88,7 +88,10 @@ public class SparkDumpFunderResults implements Serializable { } else { String fName = p.getId().substring(3, p.getId().indexOf("_")).toUpperCase(); if (fName.equalsIgnoreCase("ec")) { - if (p.getId().contains("h2020")) { + if(p.getId().contains("he")){ + fName += "_HE"; + } + else if (p.getId().contains("h2020")) { fName += "_H2020"; } else { fName += "_FP7"; diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 476ca09..57e7f9f 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.graph.dump.funderresults; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; +import java.util.Objects; import java.util.Optional; import org.apache.commons.io.IOUtils; @@ -17,6 +18,8 @@ import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Constants; import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; @@ -99,13 +102,19 @@ public class SparkResultLinkedToProject implements Serializable { .map( t2._1(), communityMap, Constants.DUMPTYPE.FUNDER.getType()); - cr.setProjects(t2._2().getProjectsList()); + if (cr != null) { + cr.setProjects(t2._2().getProjectsList()); + } return cr; }, Encoders.bean(CommunityResult.class)) + .filter(Objects::nonNull) + .map( + (MapFunction) cr -> new ObjectMapper().writeValueAsString(cr), + Encoders.STRING()) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(outputPath); + .text(outputPath); } } diff --git a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml index 46a4d32..ffa8bcd 100644 --- a/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml +++ b/dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml @@ -238,7 +238,7 @@ outputPath - ${workingDir}/tar + ${outputPath}/dump sourcePath @@ -279,7 +279,7 @@ outputPath - ${workingDir}/tar + ${outputPath}/dump @@ -299,7 +299,7 @@ outputPath - ${workingDir}/tar + ${outputPath}/dump sourcePath @@ -315,28 +315,28 @@ - - - eu.dnetlib.dhp.oa.graph.dump.MakeTar - --hdfsPath${outputPath} - --nameNode${nameNode} - --sourcePath${workingDir}/tar - - - - - - + - + + + + eu.dnetlib.dhp.oa.graph.dump.MakeTar + --hdfsPath${outputPath}/tar + --nameNode${nameNode} + --sourcePath${outputPath}/dump + + + + + ${wf:conf('upload') eq true} @@ -347,7 +347,7 @@ eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS - --hdfsPath${outputPath} + --hdfsPath${outputPath}/tar/ --nameNode${nameNode} --accessToken${accessToken} --connectionUrl${connectionUrl} diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/subset/DumpSubsetTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/subset/DumpSubsetTest.java index 5fa9286..ce73ac6 100644 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/subset/DumpSubsetTest.java +++ b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/subset/DumpSubsetTest.java @@ -456,7 +456,7 @@ public class DumpSubsetTest { getClass() .getResource("/eu/dnetlib/dhp/oa/graph/dump/subset/dump/community_infrastructure") .getPath()) - .saveAsTextFile(workingDir.toString() + "/dump/community_infrastructure"); + .saveAsTextFile(workingDir.toString() + "/dump/communities_infrastructures"); SparkSelectValidRelationContext .main( @@ -512,10 +512,12 @@ public class DumpSubsetTest { .textFile(workingDir.toString() + "/relation") .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.oa.model.graph.Relation.class)); - Assertions.assertEquals(94, tmp.count()); - Assertions.assertEquals(47, tmp.filter(r -> r.getSource().getId().startsWith("50|")).count()); - Assertions.assertEquals(36, tmp.filter(r -> r.getSource().getId().startsWith("10|")).count()); - Assertions.assertEquals(11, tmp.filter(r -> r.getSource().getId().startsWith("00|")).count()); + Assertions.assertEquals(102, tmp.count()); + + + Assertions.assertEquals(51, tmp.filter(r -> r.getSource().getId().startsWith("50|")).count()); + Assertions.assertEquals(39, tmp.filter(r -> r.getSource().getId().startsWith("10|")).count()); + Assertions.assertEquals(12, tmp.filter(r -> r.getSource().getId().startsWith("00|")).count()); } } diff --git a/dump/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/publication_extendedmodel b/dump/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/publication_extendedmodel index f198781..b56b30f 100644 --- a/dump/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/publication_extendedmodel +++ b/dump/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/publication_extendedmodel @@ -1,6 +1,2 @@ -{"author":[{"fullname":"Nikolaidou,Charitini","name":"Charitini","surname":"Nikolaidou","rank":1,"pid":null},{"fullname":"Votsi,Nefta","name":"Nefta","surname":"Votsi","rank":2,"pid":{"id":{"scheme":"orcid","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Sgardelis,Steanos","name":"Steanos","surname":"Sgardelis","rank":3,"pid":{"id":{"scheme":"orcid_pending","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Halley,John","name":"John","surname":"Halley","rank":4,"pid":null},{"fullname":"Pantis,John","name":"John","surname":"Pantis","rank":5,"pid":{"id":{"scheme":"orcid","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Tsiafouli,Maria","name":"Maria","surname":"Tsiafouli","rank":6,"pid":{"id":{"scheme":"orcid_pending","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}}],"type":"publication","language":{"code":"eng","label":"English"},"country":[{"code":"IT","label":"Italy","provenance":null}],"subjects":[{"subject":{"scheme":"ACM","value":"Ecosystem Services hotspots"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Natura 2000"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Quiet Protected Areas"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Biodiversity"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Agriculture"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Elevation"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Slope"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"Ecosystem Service trade-offs and synergies"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":" cultural services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"provisioning services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"regulating services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}},{"subject":{"scheme":"","value":"supporting services"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}],"maintitle":"Ecosystem Service capacity is higher in areas of multiple designation types","subtitle":null,"description":["The implementation of the Ecosystem Service (ES) concept into practice might be a challenging task as it has to take into account previous “traditional” policies and approaches that have evaluated nature and biodiversity differently. Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. We also investigated by PCA synergies and trade-offs among different kinds of ES and tested for correlations among landscape properties, such as elevation, aspect and slope and the ES potential. Our results show that areas with different types or multiple designations have a different capacity in providing ES. Areas of one designation type (Protected or Quiet Areas) had in general intermediate scores in most ES but scores were higher compared to areas with no designation, which displayed stronger capacity in provisioning services. Among Protected Areas and Quiet Areas the latter scored better in general. Areas that combined both designation types (Protected and Quiet Areas) showed the highest capacity in 13 out of 29 ES, that were mostly linked with natural and forest ecosystems. We found significant synergies among most regulating, supporting and cultural ES which in turn display trade-offs with provisioning services. The different ES are spatially related and display strong correlation with landscape properties, such as elevation and slope. We suggest that the designation status of an area can be used as an alternative tool for environmental policy, indicating the capacity for ES provision. Multiple designations of areas can be used as proxies for locating ES “hotspots”. This integration of “traditional” evaluation and designation and the “newer” ES concept forms a time- and cost-effective way to be adopted by stakeholders and policy-makers in order to start complying with new standards and demands for nature conservation and environmental management."],"publicationdate":"2017-01-01","publisher":"Pensoft Publishers","embargoenddate":null,"source":["One Ecosystem 2: e13718"],"format":["text/html"],"contributor":[],"coverage":[],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"container":{"name":"One 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-{"author":[{"fullname":"Nikolaidou,Charitini","name":"Charitini","surname":"Nikolaidou","rank":1,"pid":null},{"fullname":"Votsi,Nefta","name":"Nefta","surname":"Votsi","rank":2,"pid":{"id":{"scheme":"orcid","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Sgardelis,Steanos","name":"Steanos","surname":"Sgardelis","rank":3,"pid":{"id":{"scheme":"orcid_pending","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Halley,John","name":"John","surname":"Halley","rank":4,"pid":null},{"fullname":"Pantis,John","name":"John","surname":"Pantis","rank":5,"pid":{"id":{"scheme":"orcid","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}},{"fullname":"Tsiafouli,Maria","name":"Maria","surname":"Tsiafouli","rank":6,"pid":{"id":{"scheme":"orcid_pending","value":"0000-0001-6651-1178"},"provenance":{"provenance":"sysimport:crosswalk:repository","trust":"0.9"}}}],"type":"publication","language":{"code":"eng","label":"English"},"country":[{"code":"IT","label":"Italy","provenance":null}],"subjects":[{"subject":{"scheme":"ACM","value":"Ecosystem 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Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. We also investigated by PCA synergies and trade-offs among different kinds of ES and tested for correlations among landscape properties, such as elevation, aspect and slope and the ES potential. Our results show that areas with different types or multiple designations have a different capacity in providing ES. Areas of one designation type (Protected or Quiet Areas) had in general intermediate scores in most ES but scores were higher compared to areas with no designation, which displayed stronger capacity in provisioning services. Among Protected Areas and Quiet Areas the latter scored better in general. Areas that combined both designation types (Protected and Quiet Areas) showed the highest capacity in 13 out of 29 ES, that were mostly linked with natural and forest ecosystems. We found significant synergies among most regulating, supporting and cultural ES which in turn display trade-offs with provisioning services. The different ES are spatially related and display strong correlation with landscape properties, such as elevation and slope. We suggest that the designation status of an area can be used as an alternative tool for environmental policy, indicating the capacity for ES provision. Multiple designations of areas can be used as proxies for locating ES “hotspots”. 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