From 551eda1600a3a91033ab74e32ed47004f3b77b54 Mon Sep 17 00:00:00 2001 From: miconis Date: Fri, 25 Oct 2019 12:48:25 +0200 Subject: [PATCH] dataset, orp and software mapping implemented. addition of test resources for results. implementation of tests to check the result of the mapping --- .../eu/dnetlib/dhp/graph/ProtoConverter.java | 56 ++++++++++++++++--- .../java/eu/dnetlib/dhp/graph/ProtoUtils.java | 7 +++ .../dnetlib/dhp/graph/ProtoConverterTest.java | 53 ++++++++++++++++-- .../eu/dnetlib/dhp/graph/dataset.json | 1 + .../resources/eu/dnetlib/dhp/graph/orp.json | 1 + .../eu/dnetlib/dhp/graph/software.json | 1 + 6 files changed, 105 insertions(+), 14 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/graph/dataset.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/graph/orp.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/graph/software.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoConverter.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoConverter.java index fe8a87dac..600663730 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoConverter.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoConverter.java @@ -80,7 +80,7 @@ public class ProtoConverter implements Serializable { .setEcsmevalidated(mapStringField(m.getEcsmevalidated())) .setEcnutscode(mapStringField(m.getEcnutscode())) .setCountry(mapQualifier(m.getCountry())); - } + } private static Datasource convertDataSource(OafProtos.Oaf oaf) { final DatasourceProtos.Datasource.Metadata m = oaf.getEntity().getDatasource().getMetadata(); @@ -184,19 +184,47 @@ public class ProtoConverter implements Serializable { return createPublication(oaf); case "software": return createSoftware(oaf); - case "orp": + case "other": return createORP(oaf); default: - throw new RuntimeException("received unknown type :" + oaf.getEntity().getResult().getMetadata().getResulttype().getClassid()); + throw new RuntimeException("received unknown type: " + oaf.getEntity().getResult().getMetadata().getResulttype().getClassid()); } } private static Software createSoftware(OafProtos.Oaf oaf) { - return new Software(); + ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata(); + Software software = setOaf(new Software(), oaf); + setEntity(software, oaf); + return setResult(software, oaf) + .setDocumentationUrl(m.getDocumentationUrlList() + .stream() + .map(ProtoUtils::mapStringField) + .collect(Collectors.toList())) + .setLicense(m.getLicenseList() + .stream() + .map(ProtoUtils::mapStructuredProperty) + .collect(Collectors.toList())) + .setCodeRepositoryUrl(ProtoUtils.mapStringField(m.getCodeRepositoryUrl())) + .setProgrammingLanguage(ProtoUtils.mapQualifier(m.getProgrammingLanguage())); } private static OtherResearchProducts createORP(OafProtos.Oaf oaf) { - return new OtherResearchProducts(); + ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata(); + OtherResearchProducts otherResearchProducts = setOaf(new OtherResearchProducts(), oaf); + setEntity(otherResearchProducts, oaf); + return setResult(otherResearchProducts, oaf) + .setContactperson(m.getContactpersonList() + .stream() + .map(ProtoUtils::mapStringField) + .collect(Collectors.toList())) + .setContactgroup(m.getContactgroupList() + .stream() + .map(ProtoUtils::mapStringField) + .collect(Collectors.toList())) + .setTool(m.getToolList() + .stream() + .map(ProtoUtils::mapStringField) + .collect(Collectors.toList())); } private static Publication createPublication(OafProtos.Oaf oaf) { @@ -206,11 +234,23 @@ public class ProtoConverter implements Serializable { setEntity(publication, oaf); return setResult(publication, oaf) .setJournal(mapJournal(m.getJournal())); - - } private static Dataset createDataset(OafProtos.Oaf oaf) { - return new Dataset(); + + ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata(); + Dataset dataset = setOaf(new Dataset(), oaf); + setEntity(dataset, oaf); + return setResult(dataset, oaf) + .setStoragedate(ProtoUtils.mapStringField(m.getStoragedate())) + .setDevice(ProtoUtils.mapStringField(m.getDevice())) + .setSize(ProtoUtils.mapStringField(m.getSize())) + .setVersion(ProtoUtils.mapStringField(m.getVersion())) + .setLastmetadataupdate(ProtoUtils.mapStringField(m.getLastmetadataupdate())) + .setMetadataversionnumber(ProtoUtils.mapStringField(m.getMetadataversionnumber())) + .setGeolocation(m.getGeolocationList() + .stream() + .map(ProtoUtils::mapGeolocation) + .collect(Collectors.toList())); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoUtils.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoUtils.java index 0c1c0d095..e58928734 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoUtils.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/ProtoUtils.java @@ -226,4 +226,11 @@ public class ProtoUtils { } + public static GeoLocation mapGeolocation(ResultProtos.Result.GeoLocation geoLocation) { + return new GeoLocation() + .setPoint(geoLocation.getPoint()) + .setBox(geoLocation.getBox()) + .setPlace(geoLocation.getPlace()); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/graph/ProtoConverterTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/graph/ProtoConverterTest.java index 47b6f373b..4f68ca446 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/graph/ProtoConverterTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/graph/ProtoConverterTest.java @@ -1,9 +1,7 @@ package eu.dnetlib.dhp.graph; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.io.IOUtils; import static org.junit.Assert.*; import org.junit.Test; @@ -29,8 +27,6 @@ public class ProtoConverterTest { ObjectMapper mapper = new ObjectMapper(); System.out.println(mapper.writeValueAsString(result)); - - } @Test @@ -44,7 +40,52 @@ public class ProtoConverterTest { Publication p = (Publication) result; ObjectMapper mapper = new ObjectMapper(); - System.out.println(mapper.writeValueAsString(result)); + System.out.println(mapper.writeValueAsString(p)); + + } + + @Test + public void convertDatasetTest() throws Exception { + final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/graph/dataset.json")); + + Oaf result = ProtoConverter.convert(json); + + assertNotNull(result); + assertTrue(result instanceof Dataset); + Dataset d = (Dataset) result; + + ObjectMapper mapper = new ObjectMapper(); + System.out.println(mapper.writeValueAsString(d)); + + } + + @Test + public void convertORPTest() throws Exception { + final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/graph/orp.json")); + + Oaf result = ProtoConverter.convert(json); + + assertNotNull(result); + assertTrue(result instanceof OtherResearchProducts); + OtherResearchProducts orp = (OtherResearchProducts) result; + + ObjectMapper mapper = new ObjectMapper(); + System.out.println(mapper.writeValueAsString(orp)); + + } + + @Test + public void convertSoftware() throws Exception { + final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/graph/software.json")); + + Oaf result = ProtoConverter.convert(json); + + assertNotNull(result); + assertTrue(result instanceof Software); + Software s = (Software) result; + + ObjectMapper mapper = new ObjectMapper(); + System.out.println(mapper.writeValueAsString(s)); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/graph/dataset.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/graph/dataset.json new file mode 100644 index 000000000..05ba555dd --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/graph/dataset.json @@ -0,0 +1 @@ +{"kind":1,"dataInfo":{"deletedbyinference":true,"provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemename":"dnet:provenanceActions","schemeid":"dnet:provenanceActions"},"inferred":true,"inferenceprovenance":"dedup-similarity-result-levenstein","invisible":false,"trust":"0.9"},"entity":{"pid":[{"qualifier":{"classid":"doi","classname":"doi","schemename":"dnet:pid_types","schemeid":"dnet:pid_types"},"value":"10.5517/cc11xr4v"}],"result":{"instance":[{"url":["http://dx.doi.org/10.5517/cc11xr4v"],"collectedfrom":{"value":"scholExplorer","key":"10|openaire____::e034d6a11054f5ade9221ebac484e864"},"hostedby":{"value":"Unknown Repository","key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c"},"accessright":{"classid":"UNKNOWN","classname":"not available","schemename":"dnet:access_modes","schemeid":"dnet:access_modes"},"instancetype":{"classid":"0000","classname":"Unknown","schemename":"dnet:publication_resource","schemeid":"dnet:publication_resource"}}],"metadata":{"publisher":{"value":"Cambridge Crystallographic Data Centre"},"description":[{"value":"An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. 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