mirror of
https://github.com/DSpace/DSpace.git
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DataCite plugin for import
Plugin for import of external metadata from DataCite for publications. Code by @johannastaudinger, @floriangantner and @philipprumpf.
This commit is contained in:
Johanna Staudinger
committed by
Philipp Rumpf
Philipp Rumpf
parent
ec0853ddad
commit
a9cee40a15
38
dspace-api/src/main/java/org/dspace/importer/external/datacite/DataCiteFieldMapping.java
vendored
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38
dspace-api/src/main/java/org/dspace/importer/external/datacite/DataCiteFieldMapping.java
vendored
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@@ -0,0 +1,38 @@
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/**
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* The contents of this file are subject to the license and copyright
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* detailed in the LICENSE and NOTICE files at the root of the source
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* tree and available online at
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*
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* http://www.dspace.org/license/
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*/
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package org.dspace.importer.external.datacite;
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import java.util.Map;
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import javax.annotation.Resource;
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import org.dspace.importer.external.metadatamapping.AbstractMetadataFieldMapping;
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/**
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* An implementation of {@link AbstractMetadataFieldMapping}
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* Responsible for defining the mapping of the datacite metadatum fields on the DSpace metadatum fields
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*
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* @author Pasquale Cavallo (pasquale.cavallo at 4science dot it)
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* @author Florian Gantner (florian.gantner@uni-bamberg.de)
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*/
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public class DataCiteFieldMapping extends AbstractMetadataFieldMapping {
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/**
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* Defines which metadatum is mapped on which metadatum. Note that while the key must be unique it
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* only matters here for postprocessing of the value. The mapped MetadatumContributor has full control over
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* what metadatafield is generated.
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*
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* @param metadataFieldMap The map containing the link between retrieve metadata and metadata that will be set to
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* the item.
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*/
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@Override
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@Resource(name = "dataciteMetadataFieldMap")
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public void setMetadataFieldMap(Map metadataFieldMap) {
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super.setMetadataFieldMap(metadataFieldMap);
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}
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}
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@@ -0,0 +1,379 @@
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/**
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* The contents of this file are subject to the license and copyright
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* detailed in the LICENSE and NOTICE files at the root of the source
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* tree and available online at
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*
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* http://www.dspace.org/license/
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*/
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package org.dspace.importer.external.datacite;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.LinkedHashMap;
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import java.util.List;
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import java.util.concurrent.Callable;
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import javax.el.MethodNotFoundException;
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import javax.ws.rs.client.Client;
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import javax.ws.rs.client.ClientBuilder;
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import javax.ws.rs.client.Invocation;
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import javax.ws.rs.client.WebTarget;
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import javax.ws.rs.core.Response;
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import com.google.gson.Gson;
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import com.jayway.jsonpath.JsonPath;
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import com.jayway.jsonpath.ReadContext;
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import net.minidev.json.JSONArray;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.http.client.methods.HttpGet;
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import org.dspace.content.Item;
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import org.dspace.importer.external.datamodel.ImportRecord;
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import org.dspace.importer.external.datamodel.Query;
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import org.dspace.importer.external.exception.MetadataSourceException;
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import org.dspace.importer.external.service.AbstractImportMetadataSourceService;
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import org.dspace.importer.external.service.DoiCheck;
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import org.dspace.importer.external.service.components.QuerySource;
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/**
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* Implements a data source for querying Datacite
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* Mainly copied from CrossRefImportMetadataSourceServiceImpl.
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*
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* optional Affiliation informations are not part of the API request.
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* https://support.datacite.org/docs/can-i-see-more-detailed-affiliation-information-in-the-rest-api
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*
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* @author Pasquale Cavallo (pasquale.cavallo at 4science dot it)
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* @author Florian Gantner (florian.gantner@uni-bamberg.de)
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*
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*/
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public class DataCiteImportMetadataSourceServiceImpl
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extends AbstractImportMetadataSourceService<String> implements QuerySource {
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private WebTarget webTarget;
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@Override
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public String getImportSource() {
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return "datacite";
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}
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@Override
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public void init() throws Exception {
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Client client = ClientBuilder.newClient();
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webTarget = client.target("https://api.datacite.org/dois/");
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}
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@Override
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public ImportRecord getRecord(String recordId) throws MetadataSourceException {
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List<ImportRecord> records = null;
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String id = getID(recordId);
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if (StringUtils.isNotBlank(id)) {
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records = retry(new SearchByIdCallable(id));
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} else {
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records = retry(new SearchByIdCallable(recordId));
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}
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return records == null || records.isEmpty() ? null : records.get(0);
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}
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@Override
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public int getRecordsCount(String query) throws MetadataSourceException {
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String id = getID(query);
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if (StringUtils.isNotBlank(id)) {
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return retry(new DoiCheckCallable(id));
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}
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return retry(new CountByQueryCallable(query));
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}
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@Override
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public int getRecordsCount(Query query) throws MetadataSourceException {
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String id = getID(query.toString());
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if (StringUtils.isNotBlank(id)) {
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return retry(new DoiCheckCallable(id));
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}
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return retry(new CountByQueryCallable(query));
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}
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@Override
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public Collection<ImportRecord> getRecords(String query, int start, int count) throws MetadataSourceException {
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String id = getID(query.toString());
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if (StringUtils.isNotBlank(id)) {
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return retry(new SearchByIdCallable(id));
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}
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return retry(new SearchByQueryCallable(query, count, start));
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}
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@Override
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public Collection<ImportRecord> getRecords(Query query) throws MetadataSourceException {
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String id = getID(query.toString());
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if (StringUtils.isNotBlank(id)) {
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return retry(new SearchByIdCallable(id));
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}
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return retry(new SearchByQueryCallable(query));
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}
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@Override
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public ImportRecord getRecord(Query query) throws MetadataSourceException {
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List<ImportRecord> records = null;
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String id = getID(query.toString());
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if (StringUtils.isNotBlank(id)) {
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records = retry(new SearchByIdCallable(id));
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} else {
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records = retry(new SearchByIdCallable(query));
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}
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return records == null || records.isEmpty() ? null : records.get(0);
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}
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@Override
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public Collection<ImportRecord> findMatchingRecords(Query query) throws MetadataSourceException {
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String id = getID(query.toString());
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if (StringUtils.isNotBlank(id)) {
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return retry(new SearchByIdCallable(id));
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}
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return retry(new FindMatchingRecordCallable(query));
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}
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@Override
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public Collection<ImportRecord> findMatchingRecords(Item item) throws MetadataSourceException {
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throw new MethodNotFoundException("This method is not implemented for Datacite");
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}
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public String getID(String query) {
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if (DoiCheck.isDoi(query)) {
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return query;
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}
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//Workaround for encoded slashes.
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if (query.contains("%252F")) {
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query = query.replace("%252F", "/");
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}
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if (DoiCheck.isDoi(query)) {
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return query;
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}
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return StringUtils.EMPTY;
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}
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private class SearchByQueryCallable implements Callable<List<ImportRecord>> {
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private Query query;
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private SearchByQueryCallable(String queryString, Integer maxResult, Integer start) {
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query = new Query();
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query.addParameter("query", queryString);
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query.addParameter("count", maxResult);
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query.addParameter("start", start);
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}
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private SearchByQueryCallable(Query query) {
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this.query = query;
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}
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@Override
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public List<ImportRecord> call() throws Exception {
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List<ImportRecord> results = new ArrayList<>();
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HttpGet method = null;
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try {
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Integer count = query.getParameterAsClass("count", Integer.class);
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Integer start = query.getParameterAsClass("start", Integer.class);
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WebTarget local = webTarget.queryParam("query", query.getParameterAsClass("query", String.class));
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if (count != null) {
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local = local.queryParam("rows", count);
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}
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if (start != null) {
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local = local.queryParam("offset", start);
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}
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Invocation.Builder invocationBuilder = local.request();
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Response response = invocationBuilder.get();
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if (response.getStatus() != 200) {
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return null;
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}
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String responseString = response.readEntity(String.class);
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ReadContext ctx = JsonPath.parse(responseString);
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Object o = ctx.read("$.data.attributes");
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if (o.getClass().isAssignableFrom(JSONArray.class)) {
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JSONArray array = (JSONArray)o;
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int size = array.size();
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for (int index = 0; index < size; index++) {
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Gson gson = new Gson();
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String innerJson = gson.toJson(array.get(index), LinkedHashMap.class);
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results.add(transformSourceRecords(innerJson));
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}
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} else {
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results.add(transformSourceRecords(o.toString()));
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}
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return results;
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} catch (Exception e) {
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throw new RuntimeException(e.getMessage(), e);
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} finally {
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if (method != null) {
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method.releaseConnection();
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}
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}
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}
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}
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private class SearchByIdCallable implements Callable<List<ImportRecord>> {
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private Query query;
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private SearchByIdCallable(Query query) {
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this.query = query;
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}
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private SearchByIdCallable(String id) {
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this.query = new Query();
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query.addParameter("id", id);
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}
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@Override
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public List<ImportRecord> call() throws Exception {
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List<ImportRecord> results = new ArrayList<>();
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HttpGet method = null;
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try {
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WebTarget local = webTarget.path(query.getParameterAsClass("id", String.class));
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Invocation.Builder invocationBuilder = local.request();
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Response response = invocationBuilder.get();
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if (response.getStatus() != 200) {
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return null;
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}
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String responseString = response.readEntity(String.class);
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ReadContext ctx = JsonPath.parse(responseString);
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Object o = ctx.read("$.data.attributes");
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if (o.getClass().isAssignableFrom(JSONArray.class)) {
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JSONArray array = (JSONArray)o;
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int size = array.size();
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for (int index = 0; index < size; index++) {
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Gson gson = new Gson();
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String innerJson = gson.toJson(array.get(index), LinkedHashMap.class);
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results.add(transformSourceRecords(innerJson));
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}
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} else {
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Gson gson = new Gson();
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results.add(transformSourceRecords(gson.toJson(o, Object.class)));
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}
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return results;
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} catch (Exception e) {
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throw new RuntimeException(e.getMessage(), e);
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} finally {
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if (method != null) {
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method.releaseConnection();
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}
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}
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}
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}
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private class FindMatchingRecordCallable implements Callable<List<ImportRecord>> {
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private Query query;
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private FindMatchingRecordCallable(Query q) {
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query = q;
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}
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@Override
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public List<ImportRecord> call() throws Exception {
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String queryValue = query.getParameterAsClass("query", String.class);
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Integer count = query.getParameterAsClass("count", Integer.class);
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Integer start = query.getParameterAsClass("start", Integer.class);
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List<ImportRecord> results = new ArrayList<>();
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HttpGet method = null;
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try {
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WebTarget local = webTarget;
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if (queryValue != null) {
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local = local.queryParam("query", queryValue);
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}
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if (count != null) {
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local = local.queryParam("page[size]", count);
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}
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if (start != null) {
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local = local.queryParam("page[number]", start);
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}
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Invocation.Builder invocationBuilder = local.request();
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Response response = invocationBuilder.get();
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if (response.getStatus() != 200) {
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return null;
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}
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String responseString = response.readEntity(String.class);
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ReadContext ctx = JsonPath.parse(responseString);
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Object o = ctx.read("$.data.attributes");
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if (o.getClass().isAssignableFrom(JSONArray.class)) {
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JSONArray array = (JSONArray)o;
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int size = array.size();
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for (int index = 0; index < size; index++) {
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Gson gson = new Gson();
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String innerJson = gson.toJson(array.get(index), LinkedHashMap.class);
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results.add(transformSourceRecords(innerJson));
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}
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} else {
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results.add(transformSourceRecords(o.toString()));
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}
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return results;
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} catch (Exception e) {
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throw new RuntimeException(e.getMessage(), e);
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} finally {
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if (method != null) {
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method.releaseConnection();
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}
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}
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}
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}
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private class CountByQueryCallable implements Callable<Integer> {
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private Query query;
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private CountByQueryCallable(String queryString) {
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query = new Query();
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query.addParameter("query", queryString);
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}
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private CountByQueryCallable(Query query) {
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this.query = query;
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}
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@Override
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public Integer call() throws Exception {
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HttpGet method = null;
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try {
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WebTarget local = webTarget.queryParam("query", query.getParameterAsClass("query", String.class));
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Invocation.Builder invocationBuilder = local.request();
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Response response = invocationBuilder.get();
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if (response.getStatus() != 200) {
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return null;
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}
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String responseString = response.readEntity(String.class);
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ReadContext ctx = JsonPath.parse(responseString);
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return ctx.read("$.meta.total");
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} catch (Exception e) {
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throw new RuntimeException(e.getMessage(), e);
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} finally {
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if (method != null) {
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method.releaseConnection();
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}
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}
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}
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}
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private class DoiCheckCallable implements Callable<Integer> {
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private final Query query;
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private DoiCheckCallable(final String id) {
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final Query query = new Query();
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query.addParameter("id", id);
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this.query = query;
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}
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private DoiCheckCallable(final Query query) {
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this.query = query;
|
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}
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||||
|
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@Override
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public Integer call() throws Exception {
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WebTarget local = webTarget.path(query.getParameterAsClass("id", String.class));
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Invocation.Builder invocationBuilder = local.request();
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Response response = invocationBuilder.head();
|
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return response.getStatus() == 200 ? 1 : 0;
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||||
}
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||||
}
|
||||
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||||
}
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@@ -34,6 +34,14 @@
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</property>
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</bean>
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||||
|
||||
<bean id="DataCiteImportService"
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class="org.dspace.importer.external.datacite.DataCiteImportMetadataSourceServiceImpl" scope="singleton">
|
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<property name="metadataFieldMapping" ref="DataCiteMetadataFieldMapping"/>
|
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</bean>
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||||
<bean id="DataCiteMetadataFieldMapping"
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class="org.dspace.importer.external.datacite.DataCiteFieldMapping">
|
||||
</bean>
|
||||
|
||||
<bean id="ArXivImportService"
|
||||
class="org.dspace.importer.external.arxiv.service.ArXivImportMetadataSourceServiceImpl" scope="singleton">
|
||||
<property name="metadataFieldMapping" ref="ArXivMetadataFieldMapping"/>
|
||||
|
||||
@@ -91,4 +91,15 @@
|
||||
</property>
|
||||
</bean>
|
||||
|
||||
<bean id="dataciteLiveImportDataProvider" class="org.dspace.external.provider.impl.LiveImportDataProvider">
|
||||
<property name="metadataSource" ref="DataCiteImportService"/>
|
||||
<property name="sourceIdentifier" value="datacite"/>
|
||||
<property name="recordIdMetadata" value="dc.identifier.doi"/>
|
||||
<property name="supportedEntityTypes">
|
||||
<list>
|
||||
<value>Publication</value>
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||||
<value>none</value>
|
||||
</list>
|
||||
</property>
|
||||
</bean>
|
||||
</beans>
|
||||
@@ -53,7 +53,7 @@ public class ExternalSourcesRestControllerIT extends AbstractControllerIntegrati
|
||||
ExternalSourceMatcher.matchExternalSource(
|
||||
"openAIREFunding", "openAIREFunding", false)
|
||||
)))
|
||||
.andExpect(jsonPath("$.page.totalElements", Matchers.is(9)));
|
||||
.andExpect(jsonPath("$.page.totalElements", Matchers.is(10)));
|
||||
}
|
||||
|
||||
@Test
|
||||
|
||||
43
dspace/config/spring/api/datacite-integration.xml
Normal file
43
dspace/config/spring/api/datacite-integration.xml
Normal file
@@ -0,0 +1,43 @@
|
||||
<beans xmlns="http://www.springframework.org/schema/beans"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xmlns:context="http://www.springframework.org/schema/context"
|
||||
xmlns:util="http://www.springframework.org/schema/util"
|
||||
xsi:schemaLocation="http://www.springframework.org/schema/beans
|
||||
http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
|
||||
http://www.springframework.org/schema/context
|
||||
http://www.springframework.org/schema/context/spring-context-2.5.xsd http://www.springframework.org/schema/util http://www.springframework.org/schema/util/spring-util.xsd"
|
||||
default-autowire-candidates="*Service,*DAO,javax.sql.DataSource">
|
||||
|
||||
|
||||
<context:annotation-config/>
|
||||
<!-- allows us to use spring annotations in beans -->
|
||||
|
||||
<util:map id="dataciteMetadataFieldMap" key-type="org.dspace.importer.external.metadatamapping.MetadataFieldConfig"
|
||||
value-type="org.dspace.importer.external.metadatamapping.contributor.MetadataContributor">
|
||||
<description>Defines which metadatum is mapped on which metadatum. Note that while the key must be unique it
|
||||
only matters here for postprocessing of the value. The mapped MetadatumContributor has full control over
|
||||
what metadatafield is generated.
|
||||
</description>
|
||||
<entry key-ref="datacite.title" value-ref="dataciteTitleContrib"/>
|
||||
<entry key-ref="datacite.id" value-ref="dataciteIDContrib"/>
|
||||
<!-- TODO: Further Mappings here! querys are applied among the data.attributes object containing the informations -->
|
||||
</util:map>
|
||||
|
||||
<bean id="dataciteTitleContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleJsonPathMetadataContributor">
|
||||
<property name="field" ref="datacite.title"/>
|
||||
<property name="query" value="/titles"/>
|
||||
</bean>
|
||||
<bean id="datacite.title" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.title"/>
|
||||
</bean>
|
||||
|
||||
<!-- must be present to be imported, since it's used as the recordId-->
|
||||
<bean id="dataciteIDContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleJsonPathMetadataContributor">
|
||||
<property name="field" ref="datacite.id"/>
|
||||
<property name="query" value="/doi"/>
|
||||
</bean>
|
||||
<bean id="datacite.id" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.identifier.doi"/>
|
||||
</bean>
|
||||
|
||||
</beans>
|
||||
Reference in New Issue
Block a user