dataset, orp and software mapping implemented. addition of test resources for results. implementation of tests to check the result of the mapping

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()));
     }
 }

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());
+    }
+
 }

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.*;
-import eu.dnetlib.dhp.schema.oaf.Oaf;
-import eu.dnetlib.dhp.schema.oaf.Publication;
 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));
 
     }
 

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. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures."}],"language":{"classid":"und","classname":"Undetermined","schemename":"dent:languages","schemeid":"dent:languages"},"title":[{"qualifier":{"classid":"main title","classname":"main title","schemename":"dnet:dataCite_title","schemeid":"dnet:dataCite_title"},"value":"CCDC 980937: Experimental Crystal Structure Determination"}],"author":[{"fullname":"Yuan, Xian-You","rank":1},{"fullname":"Ou, Guang-Chuan","rank":2},{"fullname":"Yuan, Lin","rank":3},{"fullname":"Zhang, Xin-Yu","rank":4},{"fullname":"Zhang, Min","rank":5}],"resulttype":{"classid":"dataset","classname":"dataset","schemename":"dnet:result_typologies","schemeid":"dnet:result_typologies"},"relevantdate":[{"qualifier":{"classid":"dnet:date","classname":"dnet:date","schemename":"dnet:date","schemeid":"dnet:date"},"value":"2016-01-01"}],"subject":[{"qualifier":{"classid":"keyword","classname":"keyword","schemename":"dnet:subject","schemeid":"dnet:subject"},"value":"Experimental 3D Coordinates"},{"qualifier":{"classid":"keyword","classname":"keyword","schemename":"dnet:subject","schemeid":"dnet:subject"},"value":"Crystal Structure"},{"qualifier":{"classid":"keyword","classname":"keyword","schemename":"dnet:subject","schemeid":"dnet:subject"},"value":"(5-ethyl-2-methyl-2-phenyl-1,3-dioxan-5-yl)methanol"},{"qualifier":{"classid":"keyword","classname":"keyword","schemename":"dnet:subject","schemeid":"dnet:subject"},"value":"Crystal System"},{"qualifier":{"classid":"keyword","classname":"keyword","schemename":"dnet:subject","schemeid":"dnet:subject"},"value":"Space Group"},{"qualifier":{"classid":"keyword","classname":"keyword","schemename":"dnet:subject","schemeid":"dnet:subject"},"value":"Cell Parameters"},{"qualifier":{"classid":"keyword","classname":"keyword","schemename":"dnet:subject","schemeid":"dnet:subject"},"value":"Crystallography"}]}},"collectedfrom":[{"value":"scholExplorer","key":"10|openaire____::e034d6a11054f5ade9221ebac484e864"}],"dateofcollection":"2019-10-22T14:29:26+00:00","type":50,"id":"50|scholexplore::000023d184acb169596e3e6004abb421"}}

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/graph/orp.json

@@ -0,0 +1 @@
+{"kind":1,"dataInfo":{"trust":"0.9","invisible":false,"deletedbyinference":false,"inferred":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemename":"dnet:provenanceActions","schemeid":"dnet:provenanceActions"}},"entity":{"dateoftransformation":"","pid":[{"qualifier":{"classid":"doi","classname":"doi","schemename":"dnet:pid_types","schemeid":"dnet:pid_types"},"value":"10.3203/iwf/c-13106eng"},{"qualifier":{"classid":"doi","classname":"doi","schemename":"dnet:pid_types","schemeid":"dnet:pid_types"},"value":"https://doi.org/10.3203/iwf/c-13106eng"}],"originalId":["https://doi.org/10.3203/iwf/c-13106eng","http://dx.doi.org/10.3203/iwf/c-13106eng","10.3203/iwf/c-13106eng"],"oaiprovenance":{"originDescription":{"metadataNamespace":"","altered":true,"baseURL":"https%3A%2F%2Foai.datacite.org%2Foai","datestamp":"","harvestDate":"2019-04-03T17:58:12.853Z","identifier":"10.3203/iwf/c-13106eng"}},"result":{"instance":[{"hostedby":{"value":"Unknown Repository","key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c"},"license":{"value":""},"url":["http://dx.doi.org/10.3203/iwf/c-13106eng"],"distributionlocation":"","dateofacceptance":{"value":"2007-01-01"},"collectedfrom":{"value":"Datacite","key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254"},"accessright":{"classid":"UNKNOWN","classname":"UNKNOWN","schemename":"dnet:access_modes","schemeid":"dnet:access_modes"},"instancetype":{"classid":"0000","classname":"Unknown","schemename":"dnet:dataCite_resource","schemeid":"dnet:dataCite_resource"}}],"metadata":{"publisher":{"value":"IWF (Göttingen)"},"license":[{"value":""}],"description":[{"value":"A 2D animation explains the molecular structure of histone octamers. From the CD-ROM: BEREITER-HAHN, JÜRGEN / PETERS, WINFRIED S. (Frankfurt a. M.). The Cell IV - Nucleus of Life - From Gene to Proteins (C 7103)"}],"language":{"classid":"eng","classname":"English","schemename":"dnet:languages","schemeid":"dnet:languages"},"title":[{"qualifier":{"classid":"main title","classname":"main title","schemename":"dnet:dataCite_title","schemeid":"dnet:dataCite_title"},"value":"Histone Octamer"}],"author":[{"fullname":"IWF","rank":1}],"resulttype":{"classid":"other","classname":"other","schemename":"dnet:result_typologies","schemeid":"dnet:result_typologies"},"version":{"value":"None"},"storagedate":{"value":"2007"},"dateofacceptance":{"value":"2007-01-01"},"size":{"value":""},"subject":[{"qualifier":{"classid":"keyword","classname":"keyword","schemename":"dnet:subject_classification_typologies","schemeid":"dnet:subject_classification_typologies"},"value":"Life Sciences"},{"qualifier":{"classid":"keyword","classname":"keyword","schemename":"dnet:subject_classification_typologies","schemeid":"dnet:subject_classification_typologies"},"value":"histone"},{"qualifier":{"classid":"keyword","classname":"keyword","schemename":"dnet:subject_classification_typologies","schemeid":"dnet:subject_classification_typologies"},"value":"nucleosome"}]}},"collectedfrom":[{"value":"Datacite","key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254"}],"dateofcollection":"2018-10-28T00:39:04.337Z","type":50,"id":"50|datacite____::0000228dcefe42612ec4bd83810fe348"}}