converter from orcid work json to oaf

This commit is contained in:
Enrico Ottonello 2020-07-01 18:36:14 +02:00
parent b7b6be12a5
commit 5525f57ec8
5 changed files with 598 additions and 427 deletions

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@ -0,0 +1,420 @@
package eu.dnetlib.doiboost.orcidnodoi.oaf;
import com.google.gson.Gson;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import eu.dnetlib.dhp.common.PacePerson;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.utils.DHPUtils;
import eu.dnetlib.doiboost.orcidnodoi.SparkGenEnrichedOrcidWorks;
import eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility;
import eu.dnetlib.doiboost.orcidnodoi.util.Pair;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.*;
import java.util.stream.Collectors;
import static eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility.*;
public class OrcidWorkToOAF {
static Logger logger = LoggerFactory.getLogger(OrcidWorkToOAF.class);
public static final String ORCID = "ORCID";
public final static String orcidPREFIX = "orcid_______";
public static final String OPENAIRE_PREFIX = "openaire____";
public static final String SEPARATOR = "::";
private static Map<String, Pair<String, String>> datasources = new HashMap<String, Pair<String, String>>() {
{
put(ORCID.toLowerCase(), new Pair<>(ORCID, OPENAIRE_PREFIX + SEPARATOR + "orcid"));
}
};
// json external id will be mapped to oaf:pid/@classid Map to oaf:pid/@classname
private static Map<String, Pair<String, String>> externalIds = new HashMap<String, Pair<String, String>>() {
{
put("ark".toLowerCase(), new Pair<>("ark", "ark"));
put("arxiv".toLowerCase(), new Pair<>("arxiv", "arXiv"));
put("pmc".toLowerCase(), new Pair<>("pmc", "pmc"));
put("pmid".toLowerCase(), new Pair<>("pmid", "pmid"));
put("source-work-id".toLowerCase(), new Pair<>("orcidworkid", "orcidworkid"));
put("urn".toLowerCase(), new Pair<>("urn", "urn"));
}
};
static Map<String, Map<String, String>> typologiesMapping;
static {
try {
final String tt = IOUtils.toString(OrcidWorkToOAF.class.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/orcidnodoi/mappings/typologies.json"));
typologiesMapping = new Gson().fromJson(tt, Map.class);
} catch (final Exception e) {
logger.error("loading typologies", e);
}
}
public static final String PID_TYPES = "dnet:pid_types";
public static Oaf generatePublicationActionsFromDump(final JsonObject rootElement, final String setName) {
if (!isValid(rootElement/*, context*/)) { return null; }
Publication publication = new Publication();
final DataInfo dataInfo = new DataInfo();
dataInfo.setDeletedbyinference(false);
dataInfo.setInferred(false);
dataInfo.setTrust("0.9");
dataInfo.setProvenanceaction(
mapQualifier(
"sysimport:actionset:orcidworks-no-doi",
"sysimport:actionset:orcidworks-no-doi",
"dnet:provenanceActions",
"dnet:provenanceActions"));
publication.setDataInfo(dataInfo);
publication.setLastupdatetimestamp(new Date().getTime());
publication.setDateofcollection("2019-10-22");
publication.setDateoftransformation(DumpToActionsUtility.now_ISO8601());
// Adding external ids
externalIds.keySet().stream()
.forEach(jsonExtId -> {
final String classid = externalIds.get(jsonExtId.toLowerCase()).getValue();
final String classname = externalIds.get(jsonExtId.toLowerCase()).getKey();
final String extId = getStringValue(rootElement, jsonExtId);
if (StringUtils.isNotBlank(extId)) {
publication.getExternalReference().add(
convertExtRef(extId, classid, classname, "dnet:pid_types", "dnet:pid_types"));
}
});
// Adding source
// final String source = getStringValue(rootElement, "source");
// if (StringUtils.isNotBlank(source)) {
// metadata.addSource(StringField.newBuilder().setValue(source).build());
// }
// Adding titles
final List<String> titles = createRepeatedField(rootElement, "titles");
if (titles==null || titles.isEmpty()) {
// context.incrementCounter("filtered", "title_not_found", 1);
return null;
}
Qualifier q = mapQualifier("main title","main title","dnet:dataCite_title","dnet:dataCite_title");
publication.setTitle(
titles
.stream()
.map(t -> {
return mapStructuredProperty(t, q, null);
})
.collect(Collectors.toList()));
// Adding identifier
final String id = getStringValue(rootElement, "id");
String sourceId = null;
if (id != null) {
publication.setOriginalId(Arrays.asList(id));
sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, DHPUtils.md5(id.toLowerCase()));
} else {
String mergedTitle = titles.stream().map(Object::toString).collect(Collectors.joining(","));
sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, DHPUtils.md5(mergedTitle.toLowerCase()));
}
publication.setId(sourceId);
// Adding relevant date
settingRelevantDate(rootElement, publication, "publication_date", "issued", true);
// Adding collectedfrom
publication.setCollectedfrom(Arrays.asList(createCollectedFrom()));
// Adding type
final String type = getStringValue(rootElement, "type");
String cobjValue = "";
if (StringUtils.isNotBlank(type)) {
publication.setResourcetype(mapQualifier(type, type, "dnet:dataCite_resource", "dnet:dataCite_resource"));
final String typeValue = typologiesMapping.get(type).get("value");
cobjValue = typologiesMapping.get(type).get("cobj");
final Instance instance = new Instance();
// Adding hostedby
instance.setHostedby(createHostedBy());
// Adding url
final List<String> urls = createRepeatedField(rootElement, "urls");
if (urls!=null && !urls.isEmpty()) {
instance.setUrl(urls);
}
final String pubDate = getPublicationDate(rootElement, "publication_date");
if (StringUtils.isNotBlank(pubDate)) {
instance.setDateofacceptance(mapStringField(pubDate, null));
}
instance.setCollectedfrom(createCollectedFrom());
// Adding accessright
instance.setAccessright(mapQualifier("UNKNOWN", "UNKNOWN", "dnet:access_modes", "dnet:access_modes"));
// Adding type
instance.setInstancetype(mapQualifier(cobjValue, typeValue, "dnet:publication_resource", "dnet:publication_resource"));
publication.setInstance(Arrays.asList(instance));
} else {
// context.incrementCounter("filtered", "type_not_found", 1);
return null;
}
// Adding authors
final List<Author> authors = createAuthors(rootElement);
if (authors != null && authors.size() > 0) {
publication.setAuthor(authors);
} else {
// context.incrementCounter("filtered", "author_not_found", 1);
return null;
}
String classValue = getDefaultResulttype(cobjValue);
publication.setResulttype(mapQualifier(classValue, classValue,"dnet:result_typologies", "dnet:result_typologies"));
return publication;
}
public static List<Author> createAuthors(final JsonObject root) {
final String authorsJSONFieldName = "authors";
if (root.has(authorsJSONFieldName) && root.get(authorsJSONFieldName).isJsonArray()) {
final List<Author> authors = new ArrayList<>();
final JsonArray jsonAuthors = root.getAsJsonArray(authorsJSONFieldName);
int firstCounter = 0;
int defaultCounter = 0;
int rank = 1;
int currentRank = 0;
for (final JsonElement item : jsonAuthors) {
final JsonObject jsonAuthor = item.getAsJsonObject();
final Author author = new Author();
if (item.isJsonObject()) {
final String surname = getStringValue(jsonAuthor, "surname");
final String name = getStringValue(jsonAuthor, "name");
final String oid = getStringValue(jsonAuthor, "oid");
final String seq = getStringValue(jsonAuthor, "seq");
if (StringUtils.isNotBlank(seq)) {
if (seq.equals("first")) {
firstCounter += 1;
rank = firstCounter;
} else if (seq.equals("additional")) {
rank = currentRank + 1;
} else {
defaultCounter += 1;
rank = defaultCounter;
}
}
if (StringUtils.isNotBlank(oid)) {
author.setPid(Arrays.asList(mapAuthorId(oid)));
author.setFullname(name + " " + surname);
if (StringUtils.isNotBlank(name)) {
author.setName(name);
}
if (StringUtils.isNotBlank(surname)) {
author.setSurname(surname);
}
} else {
String fullname = "";
if (StringUtils.isNotBlank(name)) {
fullname = name;
} else {
if (StringUtils.isNotBlank(surname)) {
fullname = surname;
}
}
PacePerson p = new PacePerson(fullname, false);
if (p.isAccurate()) {
author.setName(p.getNormalisedFirstName());
author.setSurname(p.getNormalisedSurname());
author.setFullname(p.getNormalisedFullname());
}
else {
author.setFullname(fullname);
}
}
}
author.setRank(rank);
authors.add(author);
currentRank = rank;
}
return authors;
}
return null;
}
private static List<String> createRepeatedField(final JsonObject rootElement, final String fieldName) {
if (!rootElement.has(fieldName)) { return null; }
if (rootElement.has(fieldName) && rootElement.get(fieldName).isJsonNull()) { return null; }
if (rootElement.get(fieldName).isJsonArray()) {
if (!isValidJsonArray(rootElement, fieldName)) { return null; }
return getArrayValues(rootElement, fieldName);
} else {
String field = getStringValue(rootElement, fieldName);
return Arrays.asList(cleanField(field));
}
}
private static String cleanField(String value) {
if (value != null && !value.isEmpty() && value.charAt(0) == '"' && value.charAt(value.length() - 1) == '"') {
value = value.substring(1, value.length() - 1);
}
return value;
}
private static void settingRelevantDate(final JsonObject rootElement,
final Publication publication,
final String jsonKey,
final String dictionaryKey,
final boolean addToDateOfAcceptance) {
final String pubDate = getPublicationDate(rootElement, "publication_date");
if (StringUtils.isNotBlank(pubDate)) {
if (addToDateOfAcceptance) {
publication.setDateofacceptance(mapStringField(pubDate, null));
}
Qualifier q = mapQualifier(dictionaryKey,dictionaryKey,"dnet:dataCite_date","dnet:dataCite_date");
publication.setRelevantdate(
Arrays.asList(pubDate)
.stream()
.map(r -> {
return mapStructuredProperty(r, q, null);
})
.collect(Collectors.toList()));
}
}
private static String getPublicationDate(final JsonObject rootElement,
final String jsonKey) {
final JsonObject pubDateJson = rootElement.getAsJsonObject(jsonKey);
if (pubDateJson == null) { return null; }
final String year = getStringValue(pubDateJson, "year");
final String month = getStringValue(pubDateJson, "month");
final String day = getStringValue(pubDateJson, "day");
if (StringUtils.isBlank(year)) { return null; }
String pubDate = "".concat(year);
if (StringUtils.isNotBlank(month)) {
pubDate = pubDate.concat("-" + month);
if (StringUtils.isNotBlank(day)) {
pubDate = pubDate.concat("-" + day);
} else {
pubDate += "-01";
}
} else {
pubDate += "-01-01";
}
if (isValidDate(pubDate)) { return pubDate; }
return null;
}
protected static boolean isValid(final JsonObject rootElement/*, final Reporter context*/) {
final String type = getStringValue(rootElement, "type");
if (!typologiesMapping.containsKey(type)) {
// context.incrementCounter("filtered", "unknowntype_" + type, 1);
return false;
}
if (!isValidJsonArray(rootElement, "titles")) {
// context.incrementCounter("filtered", "invalid_title", 1);
return false;
}
return true;
}
private static boolean isValidJsonArray(final JsonObject rootElement, final String fieldName) {
if (!rootElement.has(fieldName)) { return false; }
final JsonElement jsonElement = rootElement.get(fieldName);
if (jsonElement.isJsonNull()) { return false; }
if (jsonElement.isJsonArray()) {
final JsonArray jsonArray = jsonElement.getAsJsonArray();
if (jsonArray.isJsonNull()) { return false; }
if (jsonArray.get(0).isJsonNull()) { return false; }
}
return true;
}
private static Qualifier mapQualifier(String classId, String className, String schemeId, String schemeName) {
final Qualifier qualifier = new Qualifier();
qualifier.setClassid(classId);
qualifier.setClassname(className);
qualifier.setSchemeid(schemeId);
qualifier.setSchemename(schemeName);
return qualifier;
}
private static ExternalReference convertExtRef(String extId, String classId, String className, String schemeId, String schemeName) {
ExternalReference ex = new ExternalReference();
ex.setRefidentifier(extId);
ex.setQualifier(mapQualifier(classId, className, schemeId, schemeName ));
return ex;
}
private static StructuredProperty mapStructuredProperty(String value, Qualifier qualifier, DataInfo dataInfo) {
if (value == null | StringUtils.isBlank(value)) {
return null;
}
final StructuredProperty structuredProperty = new StructuredProperty();
structuredProperty.setValue(value);
structuredProperty.setQualifier(qualifier);
structuredProperty.setDataInfo(dataInfo);
return structuredProperty;
}
private static Field<String> mapStringField(String value, DataInfo dataInfo) {
if (value == null || StringUtils.isBlank(value)) {
return null;
}
final Field<String> stringField = new Field<>();
stringField.setValue(value);
stringField.setDataInfo(dataInfo);
return stringField;
}
private static KeyValue createCollectedFrom() {
KeyValue cf = new KeyValue();
cf.setValue(ORCID);
cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "806360c771262b4d6770e7cdf04b5c5a");
return cf;
}
private static KeyValue createHostedBy() {
KeyValue hb = new KeyValue();
hb.setValue("Unknown Repository");
hb.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "55045bd2a65019fd8e6741a755395c8c");
return hb;
}
private static StructuredProperty mapAuthorId(String orcidId) {
final StructuredProperty sp = new StructuredProperty();
sp.setValue(orcidId);
final Qualifier q = new Qualifier();
q.setClassid("ORCID");
q.setClassname("ORCID");
sp.setQualifier(q);
return sp;
}
}

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package eu.dnetlib.doiboost.orcidnodoi.proto;
public class ProtoWriter {
}
//
//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getArrayValues;
//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getDefaultResulttype;
//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getQualifier;
//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getStringValue;
//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.isValidDate;
//
//import java.io.IOException;
//import java.io.InputStream;
//import java.util.ArrayList;
//import java.util.HashMap;
//import java.util.List;
//import java.util.Map;
//
//import org.apache.commons.io.IOUtils;
//import org.apache.commons.lang3.StringUtils;
//
//import com.google.gson.Gson;
//import com.google.gson.JsonArray;
//import com.google.gson.JsonElement;
//import com.google.gson.JsonObject;
//import com.googlecode.protobuf.format.JsonFormat;
//
//import eu.dnetlib.actionmanager.actions.ActionFactory;
//import eu.dnetlib.actionmanager.actions.AtomicAction;
//import eu.dnetlib.actionmanager.common.Agent;
//import eu.dnetlib.data.mapreduce.hbase.Reporter;
//import eu.dnetlib.data.mapreduce.util.StreamUtils;
//import eu.dnetlib.data.proto.FieldTypeProtos;
//import eu.dnetlib.data.proto.FieldTypeProtos.Author;
//import eu.dnetlib.data.proto.FieldTypeProtos.DataInfo;
//import eu.dnetlib.data.proto.FieldTypeProtos.KeyValue;
//import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
//import eu.dnetlib.data.proto.FieldTypeProtos.StringField;
//import eu.dnetlib.data.proto.FieldTypeProtos.StructuredProperty;
//import eu.dnetlib.data.proto.KindProtos;
//import eu.dnetlib.data.proto.OafProtos;
//import eu.dnetlib.data.proto.ResultProtos;
//import eu.dnetlib.data.proto.TypeProtos;
//import eu.dnetlib.data.transform.xml.AbstractDNetXsltFunctions;
//import eu.dnetlib.miscutils.collections.Pair;
//import eu.dnetlib.miscutils.datetime.DateUtils;
//import eu.dnetlib.pace.model.Person;
//
//public class ProtoWriter {
//
// public static final String ORCID = "ORCID";
// public final static String orcidPREFIX = "orcid_______";
// public static final String OPENAIRE_PREFIX = "openaire____";
// public static final String SEPARATOR = "::";
//
// private static Map<String, Pair<String, String>> datasources = new HashMap<String, Pair<String, String>>() {
//
// {
// put(ORCID.toLowerCase(), new Pair<>(ORCID, OPENAIRE_PREFIX + SEPARATOR + "orcid"));
//
// }
// };
//
// // json external id will be mapped to oaf:pid/@classid Map to oaf:pid/@classname
// private static Map<String, Pair<String, String>> externalIds = new HashMap<String, Pair<String, String>>() {
//
// {
// put("ark".toLowerCase(), new Pair<>("ark", "ark"));
// put("arxiv".toLowerCase(), new Pair<>("arxiv", "arXiv"));
// put("pmc".toLowerCase(), new Pair<>("pmc", "pmc"));
// put("pmid".toLowerCase(), new Pair<>("pmid", "pmid"));
// put("source-work-id".toLowerCase(), new Pair<>("orcidworkid", "orcidworkid"));
// put("urn".toLowerCase(), new Pair<>("urn", "urn"));
// }
// };
//
// static Map<String, Map<String, String>> typologiesMapping;
//
// static {
// try {
// final InputStream is = OrcidToActions.class.getResourceAsStream("/eu/dnetlib/data/mapreduce/hbase/dataimport/mapping_typologies_orcid.json");
// final String tt = IOUtils.toString(is);
// typologiesMapping = new Gson().fromJson(tt, Map.class);
// } catch (final IOException e) {
// e.printStackTrace();
// }
// }
//
// public static final String PID_TYPES = "dnet:pid_types";
//
// public static List<AtomicAction> generatePublicationActionsFromDump(final JsonObject rootElement,
// final ActionFactory factory,
// final String setName,
// final Agent agent,
// final Reporter context) {
//
// if (!isValid(rootElement, context)) { return null; }
//
// // Create OAF proto
//
// final OafProtos.Oaf.Builder oaf = OafProtos.Oaf.newBuilder();
//
// oaf.setDataInfo(
// DataInfo.newBuilder()
// .setDeletedbyinference(false)
// .setInferred(false)
// .setTrust("0.9")
// .setProvenanceaction(getQualifier("sysimport:actionset:orcidworks-no-doi", "dnet:provenanceActions"))
// .build());
//
// // Adding kind
// oaf.setKind(KindProtos.Kind.entity);
//
// oaf.setLastupdatetimestamp(DateUtils.now());
//
// // creating result proto
// final OafProtos.OafEntity.Builder entity = OafProtos.OafEntity.newBuilder().setType(TypeProtos.Type.result);
//
// entity.setDateofcollection("2018-10-22");
// entity.setDateoftransformation(DateUtils.now_ISO8601());
//
// // Adding external ids
// StreamUtils.toStream(externalIds.keySet().iterator())
// .forEach(jsonExtId -> {
// final String classid = externalIds.get(jsonExtId.toLowerCase()).getValue();
// final String classname = externalIds.get(jsonExtId.toLowerCase()).getKey();
// final String extId = getStringValue(rootElement, jsonExtId);
// if (StringUtils.isNotBlank(extId)) {
// entity.addPid(StructuredProperty.newBuilder()
// .setValue(extId)
// .setQualifier(Qualifier.newBuilder().setClassid(classid).setClassname(classname).setSchemeid("dnet:pid_types")
// .setSchemename("dnet:pid_types").build())
// .build());
// }
// });
//
// // Create result field
// final ResultProtos.Result.Builder result = ResultProtos.Result.newBuilder();
//
// // Create metadata proto
// final ResultProtos.Result.Metadata.Builder metadata = ResultProtos.Result.Metadata.newBuilder();
//
// // Adding source
// final String source = getStringValue(rootElement, "source");
// if (StringUtils.isNotBlank(source)) {
// metadata.addSource(StringField.newBuilder().setValue(source).build());
// }
//
// // Adding title
// final String title = createRepeatedField(rootElement, "titles");
// if (StringUtils.isBlank(title)) {
// context.incrementCounter("filtered", "title_not_found", 1);
// return null;
// }
// metadata.addTitle(FieldTypeProtos.StructuredProperty.newBuilder()
// .setValue(title)
// .setQualifier(getQualifier("main title", "dnet:dataCite_title"))
// .build());
//
// // Adding identifier
// final String id = getStringValue(rootElement, "id");
// String sourceId = null;
// if (id != null) {
// entity.addOriginalId(id);
// sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, AbstractDNetXsltFunctions.md5(id));
// } else {
// sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, AbstractDNetXsltFunctions.md5(title));
// }
// entity.setId(sourceId);
//
// // Adding relevant date
// settingRelevantDate(rootElement, metadata, "publication_date", "issued", true);
//
// // Adding collectedfrom
// final FieldTypeProtos.KeyValue collectedFrom = FieldTypeProtos.KeyValue.newBuilder()
// .setValue(ORCID)
// .setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "806360c771262b4d6770e7cdf04b5c5a")
// .build();
// entity.addCollectedfrom(collectedFrom);
//
// // Adding type
// final String type = getStringValue(rootElement, "type");
// String cobjValue = "";
// if (StringUtils.isNotBlank(type)) {
//
// metadata.setResourcetype(FieldTypeProtos.Qualifier.newBuilder()
// .setClassid(type)
// .setClassname(type)
// .setSchemeid("dnet:dataCite_resource")
// .setSchemename("dnet:dataCite_resource")
// .build());
//
// final String typeValue = typologiesMapping.get(type).get("value");
// cobjValue = typologiesMapping.get(type).get("cobj");
// final ResultProtos.Result.Instance.Builder instance = ResultProtos.Result.Instance.newBuilder();
//
// // Adding hostedby
// instance.setHostedby(FieldTypeProtos.KeyValue.newBuilder()
// .setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "55045bd2a65019fd8e6741a755395c8c")
// .setValue("Unknown Repository")
// .build());
//
// // Adding url
// final String url = createRepeatedField(rootElement, "urls");
// if (StringUtils.isNotBlank(url)) {
// instance.addUrl(url);
// }
//
// final String pubDate = getPublicationDate(rootElement, "publication_date");
// if (StringUtils.isNotBlank(pubDate)) {
// instance.setDateofacceptance(FieldTypeProtos.StringField.newBuilder().setValue(pubDate).build());
// }
//
// instance.setCollectedfrom(collectedFrom);
//
// // Adding accessright
// instance.setAccessright(FieldTypeProtos.Qualifier.newBuilder()
// .setClassid("UNKNOWN")
// .setClassname("UNKNOWN")
// .setSchemeid("dnet:access_modes")
// .setSchemename("dnet:access_modes")
// .build());
//
// // Adding type
// instance.setInstancetype(FieldTypeProtos.Qualifier.newBuilder()
// .setClassid(cobjValue)
// .setClassname(typeValue)
// .setSchemeid("dnet:publication_resource")
// .setSchemename("dnet:publication_resource")
// .build());
//
// result.addInstance(instance);
// } else {
// context.incrementCounter("filtered", "type_not_found", 1);
// return null;
// }
//
// // Adding authors
// final List<Author> authors = createAuthors(rootElement);
// if (authors != null && authors.size() > 0) {
// metadata.addAllAuthor(authors);
// } else {
// context.incrementCounter("filtered", "author_not_found", 1);
// return null;
// }
//
// metadata.setResulttype(getQualifier(getDefaultResulttype(cobjValue), "dnet:result_typologies"));
// result.setMetadata(metadata.build());
// entity.setResult(result.build());
// oaf.setEntity(entity.build());
//
// final List<AtomicAction> actionList = new ArrayList<>();
//
// actionList.add(factory.createAtomicAction(setName, agent, oaf.getEntity().getId(), "result", "body", oaf.build().toByteArray()));
//
//// System.out.println(JsonFormat.printToString(oaf.build()));
// return actionList;
//
// }
//
// public static List<Author> createAuthors(final JsonObject root) {
//
// final String authorsJSONFieldName = "authors";
//
// if (root.has(authorsJSONFieldName) && root.get(authorsJSONFieldName).isJsonArray()) {
//
// final List<Author> authors = new ArrayList<>();
// final JsonArray jsonAuthors = root.getAsJsonArray(authorsJSONFieldName);
// int firstCounter = 0;
// int defaultCounter = 0;
// int rank = 1;
// int currentRank = 0;
//
// for (final JsonElement item : jsonAuthors) {
// final JsonObject author = item.getAsJsonObject();
// final Author.Builder result = Author.newBuilder();
// if (item.isJsonObject()) {
// final String surname = getStringValue(author, "surname");
// final String name = getStringValue(author, "name");
// final String oid = getStringValue(author, "oid");
// final String seq = getStringValue(author, "seq");
// if (StringUtils.isNotBlank(seq)) {
// if (seq.equals("first")) {
// firstCounter += 1;
// rank = firstCounter;
//
// } else if (seq.equals("additional")) {
// rank = currentRank + 1;
// } else {
// defaultCounter += 1;
// rank = defaultCounter;
// }
// }
//
// if (StringUtils.isNotBlank(oid)) {
// result.addPid(KeyValue.newBuilder()
// .setValue(oid)
// .setKey("ORCID")
// .build());
// result.setFullname(name + " " + surname);
// if (StringUtils.isNotBlank(name)) {
// result.setName(name);
// }
// if (StringUtils.isNotBlank(surname)) {
// result.setSurname(surname);
// }
// } else {
// String fullname = "";
// if (StringUtils.isNotBlank(name)) {
// fullname = name;
// } else {
// if (StringUtils.isNotBlank(surname)) {
// fullname = surname;
// }
// }
// Person p = new Person(fullname, false);
// if (p.isAccurate()) {
// result.setName(p.getNormalisedFirstName());
// result.setSurname(p.getNormalisedSurname());
// result.setFullname(p.getNormalisedFullname());
// }
// else {
// result.setFullname(fullname);
// }
// }
// }
// result.setRank(rank);
// authors.add(result.build());
// currentRank = rank;
// }
// return authors;
//
// }
// return null;
// }
//
// private static String createRepeatedField(final JsonObject rootElement, final String fieldName) {
// String field = "";
// if (!rootElement.has(fieldName)) { return null; }
// if (rootElement.has(fieldName) && rootElement.get(fieldName).isJsonNull()) { return null; }
// if (rootElement.get(fieldName).isJsonArray()) {
// if (!isValidJsonArray(rootElement, fieldName)) { return null; }
// final StringBuilder ttl = new StringBuilder();
// getArrayValues(rootElement, fieldName).forEach(ttl::append);
// field = ttl.toString();
// } else {
// field = getStringValue(rootElement, fieldName);
// }
//
// if (field != null && !field.isEmpty() && field.charAt(0) == '"' && field.charAt(field.length() - 1) == '"') {
// field = field.substring(1, field.length() - 1);
// }
// return field;
// }
//
// private static void settingRelevantDate(final JsonObject rootElement,
// final ResultProtos.Result.Metadata.Builder metadata,
// final String jsonKey,
// final String dictionaryKey,
// final boolean addToDateOfAcceptance) {
//
// final String pubDate = getPublicationDate(rootElement, "publication_date");
// if (StringUtils.isNotBlank(pubDate)) {
// if (addToDateOfAcceptance) {
// metadata.setDateofacceptance(FieldTypeProtos.StringField.newBuilder().setValue(pubDate).build());
// }
// metadata.addRelevantdate(FieldTypeProtos.StructuredProperty.newBuilder()
// .setValue(pubDate)
// .setQualifier(getQualifier(dictionaryKey, "dnet:dataCite_date"))
// .build());
// }
// }
//
// private static String getPublicationDate(final JsonObject rootElement,
// final String jsonKey) {
//
// final JsonObject pubDateJson = rootElement.getAsJsonObject(jsonKey);
// if (pubDateJson == null) { return null; }
// final String year = getStringValue(pubDateJson, "year");
// final String month = getStringValue(pubDateJson, "month");
// final String day = getStringValue(pubDateJson, "day");
//
// if (StringUtils.isBlank(year)) { return null; }
// String pubDate = "".concat(year);
// if (StringUtils.isNotBlank(month)) {
// pubDate = pubDate.concat("-" + month);
// if (StringUtils.isNotBlank(day)) {
// pubDate = pubDate.concat("-" + day);
// } else {
// pubDate += "-01";
// }
// } else {
// pubDate += "-01-01";
// }
// if (isValidDate(pubDate)) { return pubDate; }
// return null;
// }
//
// protected static boolean isValid(final JsonObject rootElement, final Reporter context) {
//
// final String type = getStringValue(rootElement, "type");
// if (!typologiesMapping.containsKey(type)) {
// context.incrementCounter("filtered", "unknowntype_" + type, 1);
// return false;
// }
//
// if (!isValidJsonArray(rootElement, "titles")) {
// context.incrementCounter("filtered", "invalid_title", 1);
// return false;
// }
// return true;
// }
//
// private static boolean isValidJsonArray(final JsonObject rootElement, final String fieldName) {
// if (!rootElement.has(fieldName)) { return false; }
// final JsonElement jsonElement = rootElement.get(fieldName);
// if (jsonElement.isJsonNull()) { return false; }
// if (jsonElement.isJsonArray()) {
// final JsonArray jsonArray = jsonElement.getAsJsonArray();
// if (jsonArray.isJsonNull()) { return false; }
// if (jsonArray.get(0).isJsonNull()) { return false; }
// }
// return true;
// }
//}

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@ -0,0 +1,107 @@
package eu.dnetlib.doiboost.orcidnodoi.util;
import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
import org.apache.commons.lang3.StringUtils;
import java.text.SimpleDateFormat;
import java.util.*;
public class DumpToActionsUtility {
private static final SimpleDateFormat ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US);
public static String getStringValue(final JsonObject root, final String key) {
if (root.has(key) && !root.get(key).isJsonNull())
return root.get(key).getAsString();
return null;
}
public static List<String> getArrayValues(final JsonObject root, final String key) {
if (root.has(key) && root.get(key).isJsonArray()) {
final JsonArray asJsonArray = root.get(key).getAsJsonArray();
final List<String> result = new ArrayList<>();
asJsonArray.forEach(it -> {
if (StringUtils.isNotBlank(it.getAsString())) {
result.add(it.getAsString());
}
});
return result;
}
return new ArrayList<>();
}
public static List<JsonObject> getArrayObjects(final JsonObject root, final String key) {
if (root.has(key) && root.get(key).isJsonArray()) {
final JsonArray asJsonArray = root.get(key).getAsJsonArray();
final List<JsonObject> result = new ArrayList<>();
asJsonArray.forEach(it -> {
if (it.getAsJsonObject() != null) {
result.add(it.getAsJsonObject());
}
});
return result;
}
return new ArrayList<>();
}
public static boolean isValidDate(final String date) {
return date.matches("\\d{4}-\\d{2}-\\d{2}");
}
public static String now_ISO8601() { // NOPMD
String result;
synchronized (ISO8601FORMAT) {
result = ISO8601FORMAT.format(new Date());
}
//convert YYYYMMDDTHH:mm:ss+HH00 into YYYYMMDDTHH:mm:ss+HH:00
//- note the added colon for the Timezone
return result.substring(0, result.length() - 2) + ":" + result.substring(result.length() - 2);
}
public static String getDefaultResulttype(final String cobjcategory) {
switch (cobjcategory) {
case "0029":
return "software";
case "0021":
case "0024":
case "0025":
case "0030":
return "dataset";
case "0000":
case "0010":
case "0018":
case "0020":
case "0022":
case "0023":
case "0026":
case "0027":
case "0028":
case "0037":
return "other";
case "0001":
case "0002":
case "0004":
case "0005":
case "0006":
case "0007":
case "0008":
case "0009":
case "0011":
case "0012":
case "0013":
case "0014":
case "0015":
case "0016":
case "0017":
case "0019":
case "0031":
case "0032":
return "publication";
default:
return "publication";
}
}
}

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package eu.dnetlib.doiboost.orcidnodoi.util;
public class Pair<K, V> {
private K k;
private V v;
public Pair(K k, V v) {
this.k = k;
this.v = v;
}
public K getKey() {
return k;
}
public V getValue() {
return v;
}
@Override
public boolean equals(Object obj) {
if (obj instanceof Pair<?, ?>) {
Pair<?, ?> tmp = (Pair<?, ?>) obj;
return k.equals(tmp.getKey()) && v.equals(tmp.getValue());
} else return false;
}
}

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{
"reference-entry": {"cobj":"0013", "value": "Part of book or chapter of book"},
"report": {"cobj":"0017", "value": "Report"},
"dataset": {"cobj":"0021", "value": "Dataset"},
"journal-article": {"cobj":"0001", "value": "Article"},
"reference-book": {"cobj":"0002", "value": "Book"},
"other": {"cobj":"0020", "value": "Other ORP type"},
"proceedings-article": {"cobj":"0004", "value": "Conference object"},
"standard": {"cobj":"0038", "value": "Other literature type"},
"book-part": {"cobj":"0002", "value": "Book"},
"monograph": {"cobj":"0002", "value": "Book"},
"report-series": {"cobj":"0017", "value": "Report"},
"book": {"cobj":"0002", "value": "Book"},
"book-chapter": {"cobj":"0013", "value": "Part of book or chapter of book"},
"peer-review": {"cobj":"0015", "value": "Review"},
"book-section": {"cobj":"0013", "value": "Part of book or chapter of book"},
"book-review": {"cobj":"0015", "value": "Review"},
"conference-abstract": {"cobj":"0004", "value": "Conference object"},
"conference-paper": {"cobj":"0004", "value": "Conference object"},
"conference-poster": {"cobj":"0004", "value": "Conference object"},
"data-set": {"cobj":"0021", "value": "Dataset"},
"dictionary-entry": {"cobj":"0038", "value": "Other literature type"},
"disclosure": {"cobj":"0038", "value": "Other literature type"},
"dissertation": {"cobj":"0006", "value": "Doctoral thesis"},
"edited-book": {"cobj":"0002", "value": "Book"},
"encyclopedia-entry": {"cobj":"0038", "value": "Other literature type"},
"lecture-speech": {"cobj":"0010", "value": "Lecture"},
"license": {"cobj":"0038", "value": "Other literature type"},
"magazine-article": {"cobj":"0005", "value": "Contribution for newspaper or weekly magazine"},
"manual": {"cobj":"0038", "value": "Other literature type"},
"newsletter-article": {"cobj":"0012", "value": "Newsletter"},
"newspaper-article": {"cobj":"0005", "value": "Contribution for newspaper or weekly magazine"},
"patent": {"cobj":"0019", "value": "Patent"},
"research-technique": {"cobj":"0020", "value": "Other ORP type"},
"research-tool": {"cobj":"0020", "value": "Other ORP type"},
"standards-and-policy": {"cobj":"0038", "value": "Other literature type"},
"supervised-student-publication": {"cobj":"0001", "value": "Article"},
"technical-standard": {"cobj":"0038", "value": "Other literature type"},
"website": {"cobj":"0020", "value": "Other ORP type"},
"working-paper": {"cobj":"0014", "value": "Research"}
}