From 3da12be81f19f64b9a21bdf1db2e60256395eb6b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 22 Jun 2020 19:14:06 +0200 Subject: [PATCH] - --- .../dhp/oa/graph/dump/gcat/Mapper.java | 49 ++++++------------- .../dump/gcat/SparkDumpRISISCatalogue.java | 2 +- .../dhp/oa/graph/gcat/oozie_app/workflow.xml | 8 +-- .../dhp/oa/graph/gcat/DumpJobTest.java | 6 +-- .../dhp/oa/graph/dump/gcat/software.json | 6 +++ 5 files changed, 29 insertions(+), 42 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/gcat/software.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/gcat/Mapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/gcat/Mapper.java index 29145b5a46..9478b49515 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/gcat/Mapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/gcat/Mapper.java @@ -35,11 +35,13 @@ public class Mapper implements Serializable { externals.add(kv); } out.setUrl(Constants.PUBLICATION_URL + input.getId().substring(3)); + externals.add(KeyValue.newInstance("result type", "publication")); break; case "dataset": eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input; Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); out.setUrl(Constants.DATASET_URL + input.getId().substring(3)); + externals.add(KeyValue.newInstance("result type", "dataset")); break; case "software": @@ -59,10 +61,12 @@ public class Mapper implements Serializable { .ifPresent( value -> externals.add(KeyValue.newInstance("programming language", value.getClassname()))); out.setUrl(Constants.SOFTWARE_URL + input.getId().substring(3)); + externals.add(KeyValue.newInstance("result type", "software")); break; case "other": out.setUrl(Constants.ORP_URL + input.getId().substring(3)); + externals.add(KeyValue.newInstance("result type", "other")); break; } @@ -100,13 +104,10 @@ public class Mapper implements Serializable { final List descriptionList = new ArrayList<>(); Optional .ofNullable(input.getDescription()) - .ifPresent(value -> { - Iterator> it = value.iterator(); - if (it.hasNext()) { - out.setName(it.next().getValue()); - } - it.forEachRemaining(v -> externals.add(KeyValue.newInstance("description", v.getValue()))); - }); + .ifPresent(value -> + + getDescription(out, externals, value) + ); Optional .ofNullable(input.getEmbargoenddate()) @@ -133,7 +134,6 @@ public class Mapper implements Serializable { .ofNullable(v.getUrl()) .ifPresent(u -> u.forEach(url -> urlSet.add(url))); - })); Optional @@ -180,7 +180,6 @@ public class Mapper implements Serializable { .add( KeyValue .newInstance("subject", s.getQualifier().getClassid() + ":" + s.getValue())))); - externals.add(KeyValue.newInstance("resource type", input.getResourcetype().getClassid())); cfSet.forEach(cf -> externals.add(KeyValue.newInstance("collected from", cf))); hbSet.forEach(hb -> externals.add(KeyValue.newInstance("hosted by", hb))); @@ -193,31 +192,13 @@ public class Mapper implements Serializable { return out; } - private static eu.dnetlib.dhp.schema.dump.oaf.Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) { - eu.dnetlib.dhp.schema.dump.oaf.Author a = new eu.dnetlib.dhp.schema.dump.oaf.Author(); - Optional - .ofNullable(oa.getAffiliation()) - .ifPresent( - value -> a - .setAffiliation( - value - .stream() - .map(aff -> aff.getValue()) - .collect(Collectors.toList()))); - a.setFullname(oa.getFullname()); - a.setName(oa.getName()); - a.setSurname(oa.getSurname()); - a.setRank(oa.getRank()); - Optional - .ofNullable(oa.getPid()) - .ifPresent( - value -> a - .setPid( - value - .stream() - .map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) - .collect(Collectors.toList()))); - return a; + private static void getDescription(CatalogueEntry out, List externals, List> value) { + Iterator> it = value.iterator(); + if (it.hasNext()) { + out.setNotes(it.next().getValue()); + } + it.forEachRemaining(v -> externals.add(KeyValue.newInstance("description", v.getValue()))); } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/gcat/SparkDumpRISISCatalogue.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/gcat/SparkDumpRISISCatalogue.java index 0f57879fba..1e3673e192 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/gcat/SparkDumpRISISCatalogue.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/gcat/SparkDumpRISISCatalogue.java @@ -92,7 +92,7 @@ public class SparkDumpRISISCatalogue implements Serializable { value -> execMap(value, communityName), Encoders.bean(eu.dnetlib.dhp.schema.dump.gcat.CatalogueEntry.class)) .filter(Objects::nonNull) - .repartition(1) + .repartition(1) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/gcat/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/gcat/oozie_app/workflow.xml index 9593e64d99..18a4248a71 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/gcat/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/gcat/oozie_app/workflow.xml @@ -122,7 +122,7 @@ --sourcePath${sourcePath}/publication --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/publication + --outputPath${outputPath}/publication --communityName${communityName} @@ -148,7 +148,7 @@ --sourcePath${sourcePath}/dataset --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/dataset + --outputPath${outputPath}/dataset --communityName${communityName} @@ -174,7 +174,7 @@ --sourcePath${sourcePath}/otherresearchproduct --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/otherresearchproduct + --outputPath${outputPath}/otherresearchproduct --communityName${communityName} @@ -200,7 +200,7 @@ --sourcePath${sourcePath}/software --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/software + --outputPath${outputPath}/software --communityName${communityName} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/gcat/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/gcat/DumpJobTest.java index 1678c0bdb7..df37816d20 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/gcat/DumpJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/gcat/DumpJobTest.java @@ -69,17 +69,17 @@ public class DumpJobTest { } @Test - public void testDataset() throws Exception { + public void testSoftware() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset.json") + .getResource("/eu/dnetlib/dhp/oa/graph/dump/gcat/software.json") .getPath(); SparkDumpRISISCatalogue.main(new String[] { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-outputPath", workingDir.toString() + "/result", "-sourcePath", sourcePath, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software", "-communityName", "risis" }); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/gcat/software.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/gcat/software.json new file mode 100644 index 0000000000..88c8cae3c8 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/gcat/software.json @@ -0,0 +1,6 @@ +{"author":[],"bestaccessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"codeRepositoryUrl":null,"collectedfrom":[{"dataInfo":null,"key":"10|rest________::b8e502674c3c3499d5374e9b2ea6d8d5","value":"bio.tools"}],"context":[{"dataInfo":[{"deletedbyinference":false,"inferenceprovenance":"bulktagging","inferred":true,"invisible":false,"provenanceaction":{"classid":"community:subject","classname":"Bulktagging for Community - Subject","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":null}],"id":"risis"}],"contributor":[],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2017-05-01"},"dateofcollection":"","dateoftransformation":"2020-05-27T11:24:44.113Z","description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Chilibot searches the PubMed literature database based on specific relationships between proteins, genes, or keywords. 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