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DS-3447: ORCID v2 integration (port to master from PR#2039)

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This commit is contained in:
Tim Donohue
2018-05-10 16:38:10 -05:00
parent 8c9e6afa53
commit 032a76ddb8
31 changed files with 649 additions and 2074 deletions
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12
dspace-api/pom.xml
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@@ -734,6 +734,18 @@
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<!-- For ORCID v2 integration -->
<dependency>
<groupId>org.dspace</groupId>
<artifactId>orcid-jaxb-api</artifactId>
<version>2.1.0</version>
</dependency>
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>20180130</version>
</dependency>
</dependencies>
</project>

20
dspace-api/src/main/java/org/dspace/authority/SolrAuthorityInterface.java Normal file
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@@ -0,0 +1,20 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority;
import java.util.List;
/**
* @author Jonas Van Goolen (jonas at atmire dot com)
*/
public interface SolrAuthorityInterface {
List<AuthorityValue> queryAuthorities(String text, int max);
AuthorityValue queryAuthorityID(String id);
}

87
dspace-api/src/main/java/org/dspace/authority/orcid/Orcid.java
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@@ -1,87 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import org.dspace.authority.AuthorityValue;
import org.dspace.authority.orcid.model.Bio;
import org.dspace.authority.orcid.model.Work;
import org.dspace.authority.orcid.xml.XMLtoBio;
import org.dspace.authority.orcid.xml.XMLtoWork;
import org.dspace.authority.rest.RestSource;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.w3c.dom.Document;
/**
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public class Orcid extends RestSource {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(Orcid.class);
private static Orcid orcid;
public static Orcid getOrcid() {
if (orcid == null) {
orcid = DSpaceServicesFactory.getInstance().getServiceManager()
.getServiceByName("OrcidSource", Orcid.class);
}
return orcid;
}
private Orcid(String url) {
super(url);
}
public Bio getBio(String id) {
Document bioDocument = restConnector.get(id + "/orcid-bio");
XMLtoBio converter = new XMLtoBio();
Bio bio = converter.convert(bioDocument).get(0);
bio.setOrcid(id);
return bio;
}
public List<Work> getWorks(String id) {
Document document = restConnector.get(id + "/orcid-works");
XMLtoWork converter = new XMLtoWork();
return converter.convert(document);
}
public List<Bio> queryBio(String name, int start, int rows) {
Document bioDocument = restConnector
.get("search/orcid-bio?q=" + URLEncoder.encode("\"" + name + "\"") + "&start=" + start + "&rows=" + rows);
XMLtoBio converter = new XMLtoBio();
return converter.convert(bioDocument);
}
@Override
public List<AuthorityValue> queryAuthorities(String text, int max) {
List<Bio> bios = queryBio(text, 0, max);
List<AuthorityValue> authorities = new ArrayList<AuthorityValue>();
for (Bio bio : bios) {
authorities.add(OrcidAuthorityValue.create(bio));
}
return authorities;
}
@Override
public AuthorityValue queryAuthorityID(String id) {
Bio bio = getBio(id);
return OrcidAuthorityValue.create(bio);
}
}

328
dspace-api/src/main/java/org/dspace/authority/orcid/OrcidAuthorityValue.java
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@@ -1,328 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.UUID;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.solr.common.SolrDocument;
import org.apache.solr.common.SolrInputDocument;
import org.dspace.authority.AuthorityValue;
import org.dspace.authority.AuthorityValueServiceImpl;
import org.dspace.authority.PersonAuthorityValue;
import org.dspace.authority.orcid.model.Bio;
import org.dspace.authority.orcid.model.BioExternalIdentifier;
import org.dspace.authority.orcid.model.BioName;
import org.dspace.authority.orcid.model.BioResearcherUrl;
/**
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public class OrcidAuthorityValue extends PersonAuthorityValue {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(OrcidAuthorityValue.class);
private String orcid_id;
private Map<String, List<String>> otherMetadata = new HashMap<String, List<String>>();
private boolean update; // used in setValues(Bio bio)
/**
* Creates an instance of OrcidAuthorityValue with only uninitialized fields.
* This is meant to be filled in with values from an existing record.
* To create a brand new OrcidAuthorityValue, use create()
*/
public OrcidAuthorityValue() {
}
public OrcidAuthorityValue(SolrDocument document) {
super(document);
}
public String getOrcid_id() {
return orcid_id;
}
public void setOrcid_id(String orcid_id) {
this.orcid_id = orcid_id;
}
public Map<String, List<String>> getOtherMetadata() {
return otherMetadata;
}
public void addOtherMetadata(String label, String data) {
List<String> strings = otherMetadata.get(label);
if (strings == null) {
strings = new ArrayList<String>();
}
strings.add(data);
otherMetadata.put(label, strings);
}
@Override
public SolrInputDocument getSolrInputDocument() {
SolrInputDocument doc = super.getSolrInputDocument();
if (StringUtils.isNotBlank(getOrcid_id())) {
doc.addField("orcid_id", getOrcid_id());
}
for (String t : otherMetadata.keySet()) {
List<String> data = otherMetadata.get(t);
for (String data_entry : data) {
doc.addField("label_" + t, data_entry);
}
}
return doc;
}
@Override
public void setValues(SolrDocument document) {
super.setValues(document);
this.orcid_id = String.valueOf(document.getFieldValue("orcid_id"));
otherMetadata = new HashMap<String, List<String>>();
for (String fieldName : document.getFieldNames()) {
String labelPrefix = "label_";
if (fieldName.startsWith(labelPrefix)) {
String label = fieldName.substring(labelPrefix.length());
List<String> list = new ArrayList<String>();
Collection<Object> fieldValues = document.getFieldValues(fieldName);
for (Object o : fieldValues) {
list.add(String.valueOf(o));
}
otherMetadata.put(label, list);
}
}
}
public static OrcidAuthorityValue create() {
OrcidAuthorityValue orcidAuthorityValue = new OrcidAuthorityValue();
orcidAuthorityValue.setId(UUID.randomUUID().toString());
orcidAuthorityValue.updateLastModifiedDate();
orcidAuthorityValue.setCreationDate(new Date());
return orcidAuthorityValue;
}
/**
* Create an authority based on a given orcid bio
*
* @param bio Bio
* @return OrcidAuthorityValue
*/
public static OrcidAuthorityValue create(Bio bio) {
OrcidAuthorityValue authority = OrcidAuthorityValue.create();
authority.setValues(bio);
return authority;
}
public boolean setValues(Bio bio) {
BioName name = bio.getName();
if (updateValue(bio.getOrcid(), getOrcid_id())) {
setOrcid_id(bio.getOrcid());
}
if (updateValue(name.getFamilyName(), getLastName())) {
setLastName(name.getFamilyName());
}
if (updateValue(name.getGivenNames(), getFirstName())) {
setFirstName(name.getGivenNames());
}
if (StringUtils.isNotBlank(name.getCreditName())) {
if (!getNameVariants().contains(name.getCreditName())) {
addNameVariant(name.getCreditName());
update = true;
}
}
for (String otherName : name.getOtherNames()) {
if (!getNameVariants().contains(otherName)) {
addNameVariant(otherName);
update = true;
}
}
if (updateOtherMetadata("country", bio.getCountry())) {
addOtherMetadata("country", bio.getCountry());
}
for (String keyword : bio.getKeywords()) {
if (updateOtherMetadata("keyword", keyword)) {
addOtherMetadata("keyword", keyword);
}
}
for (BioExternalIdentifier externalIdentifier : bio.getBioExternalIdentifiers()) {
if (updateOtherMetadata("external_identifier", externalIdentifier.toString())) {
addOtherMetadata("external_identifier", externalIdentifier.toString());
}
}
for (BioResearcherUrl researcherUrl : bio.getResearcherUrls()) {
if (updateOtherMetadata("researcher_url", researcherUrl.toString())) {
addOtherMetadata("researcher_url", researcherUrl.toString());
}
}
if (updateOtherMetadata("biography", bio.getBiography())) {
addOtherMetadata("biography", bio.getBiography());
}
setValue(getName());
if (update) {
update();
}
boolean result = update;
update = false;
return result;
}
private boolean updateOtherMetadata(String label, String data) {
List<String> strings = getOtherMetadata().get(label);
boolean update;
if (strings == null) {
update = StringUtils.isNotBlank(data);
} else {
update = !strings.contains(data);
}
if (update) {
this.update = true;
}
return update;
}
private boolean updateValue(String incoming, String resident) {
boolean update = StringUtils.isNotBlank(incoming) && !incoming.equals(resident);
if (update) {
this.update = true;
}
return update;
}
@Override
public Map<String, String> choiceSelectMap() {
Map<String, String> map = super.choiceSelectMap();
map.put("orcid", getOrcid_id());
return map;
}
@Override
public String getAuthorityType() {
return "orcid";
}
@Override
public String generateString() {
String generateString = AuthorityValueServiceImpl.GENERATE + getAuthorityType() + AuthorityValueServiceImpl
.SPLIT;
if (StringUtils.isNotBlank(getOrcid_id())) {
generateString += getOrcid_id();
}
return generateString;
}
@Override
public AuthorityValue newInstance(String info) {
AuthorityValue authorityValue = null;
if (StringUtils.isNotBlank(info)) {
Orcid orcid = Orcid.getOrcid();
authorityValue = orcid.queryAuthorityID(info);
} else {
authorityValue = OrcidAuthorityValue.create();
}
return authorityValue;
}
@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}
OrcidAuthorityValue that = (OrcidAuthorityValue) o;
if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
return false;
}
return true;
}
@Override
public int hashCode() {
return orcid_id != null ? orcid_id.hashCode() : 0;
}
@Override
public boolean hasTheSameInformationAs(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}
if (!super.hasTheSameInformationAs(o)) {
return false;
}
OrcidAuthorityValue that = (OrcidAuthorityValue) o;
if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
return false;
}
for (String key : otherMetadata.keySet()) {
if (otherMetadata.get(key) != null) {
List<String> metadata = otherMetadata.get(key);
List<String> otherMetadata = that.otherMetadata.get(key);
if (otherMetadata == null) {
return false;
} else {
HashSet<String> metadataSet = new HashSet<String>(metadata);
HashSet<String> otherMetadataSet = new HashSet<String>(otherMetadata);
if (!metadataSet.equals(otherMetadataSet)) {
return false;
}
}
} else {
if (that.otherMetadata.get(key) != null) {
return false;
}
}
}
return true;
}
}

188
dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv2.java Normal file
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@@ -0,0 +1,188 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang.StringUtils;
import org.apache.http.HttpResponse;
import org.apache.http.client.HttpClient;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.log4j.Logger;
import org.dspace.authority.AuthorityValue;
import org.dspace.authority.SolrAuthorityInterface;
import org.dspace.authority.orcid.xml.XMLtoBio;
import org.dspace.authority.rest.RESTConnector;
import org.json.JSONObject;
import org.orcid.jaxb.model.record_v2.Person;
/**
* @author Jonas Van Goolen (jonas at atmire dot com)
* This class contains all methods for retrieving "Person" objects calling the ORCID (version 2) endpoints.
* Additionally, this can also create AuthorityValues based on these returned Person objects
*/
public class Orcidv2 implements SolrAuthorityInterface {
private static Logger log = Logger.getLogger(Orcidv2.class);
public RESTConnector restConnector;
private String OAUTHUrl;
private String clientId;
private String clientSecret;
private String accessToken;
/**
* Initialize the accessToken that is required for all subsequent calls to ORCID
*/
public void init() throws IOException {
if (StringUtils.isNotBlank(accessToken) && StringUtils.isNotBlank(clientSecret)) {
String authenticationParameters = "?client_id=" + clientId +
"&client_secret=" + clientSecret +
"&scope=/read-public&grant_type=client_credentials";
HttpPost httpPost = new HttpPost(OAUTHUrl + authenticationParameters);
httpPost.addHeader("Accept", "application/json");
httpPost.addHeader("Content-Type", "application/x-www-form-urlencoded");
HttpClient httpClient = HttpClientBuilder.create().build();
HttpResponse getResponse = httpClient.execute(httpPost);
InputStream is = getResponse.getEntity().getContent();
BufferedReader streamReader = new BufferedReader(new InputStreamReader(is, "UTF-8"));
JSONObject responseObject = null;
String inputStr;
while ((inputStr = streamReader.readLine()) != null && responseObject == null) {
if (inputStr.startsWith("{") && inputStr.endsWith("}") && inputStr.contains("access_token")) {
try {
responseObject = new JSONObject(inputStr);
} catch (Exception e) {
//Not as valid as I'd hoped, move along
responseObject = null;
}
}
}
if (responseObject != null && responseObject.has("access_token")) {
accessToken = (String) responseObject.get("access_token");
}
}
}
/**
* Makes an instance of the Orcidv2 class based on the provided parameters.
* This constructor is called through the spring bean initialization
*/
private Orcidv2(String url, String OAUTHUrl, String clientId, String clientSecret) {
this.restConnector = new RESTConnector(url);
this.OAUTHUrl = OAUTHUrl;
this.clientId = clientId;
this.clientSecret = clientSecret;
}
/**
* Makes an instance of the Orcidv2 class based on the provided parameters.
* This constructor is called through the spring bean initialization
*/
private Orcidv2(String url) {
this.restConnector = new RESTConnector(url);
}
/**
* Makes an instance of the AuthorityValue with the given information.
* @param text search string
* @return List<AuthorityValue>
*/
@Override
public List<AuthorityValue> queryAuthorities(String text, int max) {
List<Person> bios = queryBio(text, max);
List<AuthorityValue> result = new ArrayList<>();
for (Person person : bios) {
AuthorityValue orcidAuthorityValue = Orcidv2AuthorityValue.create(person);
if (orcidAuthorityValue != null) {
result.add(orcidAuthorityValue);
}
}
return result;
}
/**
* Create an AuthorityValue from a Person retrieved using the given orcid identifier.
* @param id orcid identifier
* @return AuthorityValue
*/
public AuthorityValue queryAuthorityID(String id) {
Person person = getBio(id);
AuthorityValue valueFromPerson = Orcidv2AuthorityValue.create(person);
return valueFromPerson;
}
/**
* Retrieve a Person object based on a given orcid identifier
* @param id orcid identifier
* @return Person
*/
public Person getBio(String id) {
log.debug("getBio called with ID=" + id);
if (!isValid(id)) {
return null;
}
InputStream bioDocument = restConnector.get(id + ((id.endsWith("/person")) ? "" : "/person"), accessToken);
XMLtoBio converter = new XMLtoBio();
Person person = converter.convertSinglePerson(bioDocument);
return person;
}
/**
* Retrieve a list of Person objects.
* @param text search string
* @param start offset to use
* @param rows how many rows to return
* @return List<Person>
*/
public List<Person> queryBio(String text, int start, int rows) {
if (rows > 100) {
throw new IllegalArgumentException("The maximum number of results to retrieve cannot exceed 100.");
}
String searchPath = "search?q=" + URLEncoder.encode(text) + "&start=" + start + "&rows=" + rows;
log.debug("queryBio searchPath=" + searchPath + " accessToken=" + accessToken);
InputStream bioDocument = restConnector.get(searchPath, accessToken);
XMLtoBio converter = new XMLtoBio();
List<Person> bios = converter.convert(bioDocument);
return bios;
}
/**
* Retrieve a list of Person objects.
* @param text search string
* @param max how many rows to return
* @return List<Person>
*/
public List<Person> queryBio(String text, int max) {
return queryBio(text, 0, max);
}
/**
* Check to see if the provided text has the correct ORCID syntax.
* Since only searching on ORCID id is allowed, this way, we filter out any queries that would return a
* blank result anyway
*/
private boolean isValid(String text) {
return StringUtils.isNotBlank(text) && text.matches(Orcidv2AuthorityValue.ORCID_ID_SYNTAX);
}
}

342
dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv2AuthorityValue.java Normal file
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@@ -0,0 +1,342 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.UUID;
import org.apache.commons.lang.StringUtils;
import org.apache.solr.common.SolrDocument;
import org.apache.solr.common.SolrInputDocument;
import org.dspace.authority.AuthorityValue;
import org.dspace.authority.AuthorityValueServiceImpl;
import org.dspace.authority.PersonAuthorityValue;
import org.dspace.utils.DSpace;
import org.orcid.jaxb.model.common_v2.ExternalId;
import org.orcid.jaxb.model.record_v2.ExternalIdentifiers;
import org.orcid.jaxb.model.record_v2.KeywordType;
import org.orcid.jaxb.model.record_v2.NameType;
import org.orcid.jaxb.model.record_v2.Person;
import org.orcid.jaxb.model.record_v2.ResearcherUrlType;
/**
* @author Jonas Van Goolen (jonas at atmire dot com)
*/
public class Orcidv2AuthorityValue extends PersonAuthorityValue {
/*
* The ORCID identifier
*/
private String orcid_id;
/*
* Map containing key-value pairs filled in by "setValues(Person person)".
* This represents all dynamic information of the object.
*/
private Map<String, List<String>> otherMetadata = new HashMap<String, List<String>>();
/**
* The syntax that the ORCID id needs to conform to
*/
public static final String ORCID_ID_SYNTAX = "\\d{4}-\\d{4}-\\d{4}-(\\d{3}X|\\d{4})";
/**
* Creates an instance of Orcidv2AuthorityValue with only uninitialized fields.
* This is meant to be filled in with values from an existing record.
* To create a brand new Orcidv2AuthorityValue, use create()
*/
public Orcidv2AuthorityValue() {
}
public Orcidv2AuthorityValue(SolrDocument document) {
super(document);
}
public String getOrcid_id() {
return orcid_id;
}
public void setOrcid_id(String orcid_id) {
this.orcid_id = orcid_id;
}
/**
* Create an empty authority.
* @return OrcidAuthorityValue
*/
public static Orcidv2AuthorityValue create() {
Orcidv2AuthorityValue orcidAuthorityValue = new Orcidv2AuthorityValue();
orcidAuthorityValue.setId(UUID.randomUUID().toString());
orcidAuthorityValue.updateLastModifiedDate();
orcidAuthorityValue.setCreationDate(new Date());
return orcidAuthorityValue;
}
/**
* Create an authority based on a given orcid bio
* @return OrcidAuthorityValue
*/
public static Orcidv2AuthorityValue create(Person person) {
if (person == null) {
return null;
}
Orcidv2AuthorityValue authority = Orcidv2AuthorityValue.create();
authority.setValues(person);
return authority;
}
/**
* Initialize this instance based on a Person object
* @param person Person
*/
protected void setValues(Person person) {
NameType name = person.getName();
if (!StringUtils.equals(name.getPath(), this.getOrcid_id())) {
this.setOrcid_id(name.getPath());
}
if (!StringUtils.equals(name.getFamilyName().getValue(), this.getLastName())) {
this.setLastName(name.getFamilyName().getValue());
}
if (!StringUtils.equals(name.getGivenNames().getValue(), this.getFirstName())) {
this.setFirstName(name.getGivenNames().getValue());
}
if (name.getCreditName() != null && StringUtils.isNotBlank(name.getCreditName().getValue())) {
if (!this.getNameVariants().contains(name.getCreditName().getValue())) {
this.addNameVariant(name.getCreditName().getValue());
}
}
if (person.getKeywords() != null) {
for (KeywordType keyword : person.getKeywords().getKeyword()) {
if (this.isNewMetadata("keyword", keyword.getContent())) {
this.addOtherMetadata("keyword", keyword.getContent());
}
}
}
ExternalIdentifiers externalIdentifiers = person.getExternalIdentifiers();
if (externalIdentifiers != null) {
for (ExternalId externalIdentifier : externalIdentifiers.getExternalIdentifier()) {
if (this.isNewMetadata("external_identifier", externalIdentifier.getExternalIdValue())) {
this.addOtherMetadata("external_identifier", externalIdentifier.getExternalIdValue());
}
}
}
if (person.getResearcherUrls() != null) {
for (ResearcherUrlType researcherUrl : person.getResearcherUrls().getResearcherUrl()) {
if (this.isNewMetadata("researcher_url", researcherUrl.getUrl().getValue())) {
this.addOtherMetadata("researcher_url", researcherUrl.getUrl().getValue());
}
}
}
if (person.getBiography() != null) {
if (this.isNewMetadata("biography", person.getBiography().getContent())) {
this.addOtherMetadata("biography", person.getBiography().getContent());
}
}
this.setValue(this.getName());
}
/**
* Makes an instance of the AuthorityValue with the given information.
* @param info string info
* @return AuthorityValue
*/
@Override
public AuthorityValue newInstance(String info) {
AuthorityValue authorityValue = null;
if (StringUtils.isNotBlank(info)) {
Orcidv2 orcid = new DSpace().getServiceManager().getServiceByName("AuthoritySource", Orcidv2.class);
authorityValue = orcid.queryAuthorityID(info);
} else {
authorityValue = this.create();
}
return authorityValue;
}
@Override
public void setValue(String value) {
super.setValue(value);
}
/**
* Check to see if the provided label / data pair is already present in the "otherMetadata" or not
* */
public boolean isNewMetadata(String label, String data) {
List<String> strings = getOtherMetadata().get(label);
boolean update;
if (strings == null) {
update = StringUtils.isNotBlank(data);
} else {
update = !strings.contains(data);
}
return update;
}
/**
* Add additional metadata to the otherMetadata map*/
public void addOtherMetadata(String label, String data) {
List<String> strings = otherMetadata.get(label);
if (strings == null) {
strings = new ArrayList<>();
}
strings.add(data);
otherMetadata.put(label, strings);
}
public Map<String, List<String>> getOtherMetadata() {
return otherMetadata;
}
/**
* Generate a solr record from this instance
* @return SolrInputDocument
*/
@Override
public SolrInputDocument getSolrInputDocument() {
SolrInputDocument doc = super.getSolrInputDocument();
if (StringUtils.isNotBlank(getOrcid_id())) {
doc.addField("orcid_id", getOrcid_id());
}
for (String t : otherMetadata.keySet()) {
List<String> data = otherMetadata.get(t);
for (String data_entry : data) {
doc.addField("label_" + t, data_entry);
}
}
return doc;
}
/**
* Information that can be used the choice ui
* @return map
*/
@Override
public Map<String, String> choiceSelectMap() {
Map<String, String> map = super.choiceSelectMap();
String orcid_id = getOrcid_id();
if (StringUtils.isNotBlank(orcid_id)) {
map.put("orcid", orcid_id);
}
return map;
}
@Override
public String getAuthorityType() {
return "orcid";
}
/**
* Provides a string that will allow this AuthorityType to be recognized and provides information to create a new
* instance to be created using public Orcidv2AuthorityValue newInstance(String info).
* @return see {@link org.dspace.authority.service.AuthorityValueService#GENERATE AuthorityValueService.GENERATE}
*/
@Override
public String generateString() {
String generateString = AuthorityValueServiceImpl.GENERATE + getAuthorityType() +
AuthorityValueServiceImpl.SPLIT;
if (StringUtils.isNotBlank(getOrcid_id())) {
generateString += getOrcid_id();
}
return generateString;
}
@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}
Orcidv2AuthorityValue that = (Orcidv2AuthorityValue) o;
if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
return false;
}
return true;
}
@Override
public int hashCode() {
return orcid_id != null ? orcid_id.hashCode() : 0;
}
/**
* The regular equals() only checks if both AuthorityValues describe the same authority.
* This method checks if the AuthorityValues have different information
* E.g. it is used to decide when lastModified should be updated.
* @param o object
* @return true or false
*/
@Override
public boolean hasTheSameInformationAs(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}
if (!super.hasTheSameInformationAs(o)) {
return false;
}
Orcidv2AuthorityValue that = (Orcidv2AuthorityValue) o;
if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
return false;
}
for (String key : otherMetadata.keySet()) {
if (otherMetadata.get(key) != null) {
List<String> metadata = otherMetadata.get(key);
List<String> otherMetadata = that.otherMetadata.get(key);
if (otherMetadata == null) {
return false;
} else {
HashSet<String> metadataSet = new HashSet<String>(metadata);
HashSet<String> otherMetadataSet = new HashSet<String>(otherMetadata);
if (!metadataSet.equals(otherMetadataSet)) {
return false;
}
}
} else {
if (that.otherMetadata.get(key) != null) {
return false;
}
}
}
return true;
}
}

112
dspace-api/src/main/java/org/dspace/authority/orcid/model/Bio.java
View File

@@ -1,112 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
import java.util.LinkedHashSet;
import java.util.Set;
/**
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public class Bio {
protected String orcid;
protected BioName name;
protected String country;
protected Set<String> keywords;
protected Set<BioExternalIdentifier> bioExternalIdentifiers;
protected Set<BioResearcherUrl> researcherUrls;
protected String biography;
public Bio() {
this.name = new BioName();
keywords = new LinkedHashSet<String>();
bioExternalIdentifiers = new LinkedHashSet<BioExternalIdentifier>();
researcherUrls = new LinkedHashSet<BioResearcherUrl>();
}
public String getOrcid() {
return orcid;
}
public void setOrcid(String orcid) {
this.orcid = orcid;
}
public BioName getName() {
return name;
}
public void setName(BioName name) {
this.name = name;
}
public String getCountry() {
return country;
}
public void setCountry(String country) {
this.country = country;
}
public Set<String> getKeywords() {
return keywords;
}
public void addKeyword(String keyword) {
this.keywords.add(keyword);
}
public Set<BioExternalIdentifier> getBioExternalIdentifiers() {
return bioExternalIdentifiers;
}
public void addExternalIdentifier(BioExternalIdentifier externalReference) {
bioExternalIdentifiers.add(externalReference);
}
public Set<BioResearcherUrl> getResearcherUrls() {
return researcherUrls;
}
public void addResearcherUrl(BioResearcherUrl researcherUrl) {
researcherUrls.add(researcherUrl);
}
public String getBiography() {
return biography;
}
public void setBiography(String biography) {
this.biography = biography;
}
@Override
public String toString() {
return "Bio{" +
"orcid='" + orcid + '\'' +
", name=" + name +
", country='" + country + '\'' +
", keywords=" + keywords +
", bioExternalIdentifiers=" + bioExternalIdentifiers +
", researcherUrls=" + researcherUrls +
", biography='" + biography + '\'' +
'}';
}
}

108
dspace-api/src/main/java/org/dspace/authority/orcid/model/BioExternalIdentifier.java
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@@ -1,108 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
/**
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public class BioExternalIdentifier {
protected String id_orcid;
protected String id_common_name;
protected String id_reference;
protected String id_url;
public BioExternalIdentifier(String id_orcid, String id_common_name, String id_reference, String id_url) {
this.id_orcid = id_orcid;
this.id_common_name = id_common_name;
this.id_reference = id_reference;
this.id_url = id_url;
}
public String getId_orcid() {
return id_orcid;
}
public void setId_orcid(String id_orcid) {
this.id_orcid = id_orcid;
}
public String getId_common_name() {
return id_common_name;
}
public void setId_common_name(String id_common_name) {
this.id_common_name = id_common_name;
}
public String getId_reference() {
return id_reference;
}
public void setId_reference(String id_reference) {
this.id_reference = id_reference;
}
public String getId_url() {
return id_url;
}
public void setId_url(String id_url) {
this.id_url = id_url;
}
@Override
public String toString() {
return "BioExternalIdentifier{" +
"id_orcid='" + id_orcid + '\'' +
", id_common_name='" + id_common_name + '\'' +
", id_reference='" + id_reference + '\'' +
", id_url='" + id_url + '\'' +
'}';
}
@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}
BioExternalIdentifier that = (BioExternalIdentifier) o;
if (id_common_name != null ? !id_common_name.equals(that.id_common_name) : that.id_common_name != null) {
return false;
}
if (id_orcid != null ? !id_orcid.equals(that.id_orcid) : that.id_orcid != null) {
return false;
}
if (id_reference != null ? !id_reference.equals(that.id_reference) : that.id_reference != null) {
return false;
}
if (id_url != null ? !id_url.equals(that.id_url) : that.id_url != null) {
return false;
}
return true;
}
@Override
public int hashCode() {
int result = id_orcid != null ? id_orcid.hashCode() : 0;
result = 31 * result + (id_common_name != null ? id_common_name.hashCode() : 0);
result = 31 * result + (id_reference != null ? id_reference.hashCode() : 0);
result = 31 * result + (id_url != null ? id_url.hashCode() : 0);
return result;
}
}

114
dspace-api/src/main/java/org/dspace/authority/orcid/model/BioName.java
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@@ -1,114 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
import java.util.ArrayList;
import java.util.List;
/**
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public class BioName {
protected String givenNames;
protected String familyName;
protected String creditName;
protected List<String> otherNames;
BioName() {
otherNames = new ArrayList<String>();
}
BioName(String givenNames, String familyName, String creditName, List<String> otherNames) {
this.givenNames = givenNames;
this.familyName = familyName;
this.creditName = creditName;
this.otherNames = otherNames;
}
public String getGivenNames() {
return givenNames;
}
public void setGivenNames(String givenNames) {
this.givenNames = givenNames;
}
public String getFamilyName() {
return familyName;
}
public void setFamilyName(String familyName) {
this.familyName = familyName;
}
public String getCreditName() {
return creditName;
}
public void setCreditName(String creditName) {
this.creditName = creditName;
}
public List<String> getOtherNames() {
return otherNames;
}
public void setOtherNames(List<String> otherNames) {
this.otherNames = otherNames;
}
@Override
public String toString() {
return "BioName{" +
"givenNames='" + givenNames + '\'' +
", familyName='" + familyName + '\'' +
", creditName='" + creditName + '\'' +
", otherNames=" + otherNames +
'}';
}
@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}
BioName bioName = (BioName) o;
if (creditName != null ? !creditName.equals(bioName.creditName) : bioName.creditName != null) {
return false;
}
if (familyName != null ? !familyName.equals(bioName.familyName) : bioName.familyName != null) {
return false;
}
if (givenNames != null ? !givenNames.equals(bioName.givenNames) : bioName.givenNames != null) {
return false;
}
if (otherNames != null ? !otherNames.equals(bioName.otherNames) : bioName.otherNames != null) {
return false;
}
return true;
}
@Override
public int hashCode() {
int result = givenNames != null ? givenNames.hashCode() : 0;
result = 31 * result + (familyName != null ? familyName.hashCode() : 0);
result = 31 * result + (creditName != null ? creditName.hashCode() : 0);
result = 31 * result + (otherNames != null ? otherNames.hashCode() : 0);
return result;
}
}

77
dspace-api/src/main/java/org/dspace/authority/orcid/model/BioResearcherUrl.java
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@@ -1,77 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
/**
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public class BioResearcherUrl {
protected String name;
protected String url;
public BioResearcherUrl(String name, String url) {
this.name = name;
this.url = url;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getUrl() {
return url;
}
public void setUrl(String url) {
this.url = url;
}
@Override
public String toString() {
return "BioResearcherUrl{" +
"name='" + name + '\'' +
", url='" + url + '\'' +
'}';
}
@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}
BioResearcherUrl that = (BioResearcherUrl) o;
if (name != null ? !name.equals(that.name) : that.name != null) {
return false;
}
if (url != null ? !url.equals(that.url) : that.url != null) {
return false;
}
return true;
}
@Override
public int hashCode() {
int result = name != null ? name.hashCode() : 0;
result = 31 * result + (url != null ? url.hashCode() : 0);
return result;
}
}

49
dspace-api/src/main/java/org/dspace/authority/orcid/model/Citation.java
View File

@@ -1,49 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
/**
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public class Citation {
private CitationType type;
private String citation;
public Citation(CitationType type, String citation) {
this.type = type;
this.citation = citation;
}
public CitationType getType() {
return type;
}
public void setType(CitationType type) {
this.type = type;
}
public String getCitation() {
return citation;
}
public void setCitation(String citation) {
this.citation = citation;
}
@Override
public String toString() {
return "Citation{" +
"type=" + type +
", citation='" + citation + '\'' +
'}';
}
}

28
dspace-api/src/main/java/org/dspace/authority/orcid/model/CitationType.java
View File

@@ -1,28 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
/**
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public enum CitationType {
FORMATTED_UNSPECIFIED,
BIBTEX,
FORMATTED_APA,
FORMATTED_HARVARD,
FORMATTED_IEEE,
FORMATTED_MLA,
FORMATTED_VANCOUVER,
FORMATTED_CHICAGO
}

111
dspace-api/src/main/java/org/dspace/authority/orcid/model/Contributor.java
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@@ -1,111 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
import java.util.Set;
/**
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public class Contributor {
private String orcid;
private String creditName;
private String email;
private Set<ContributorAttribute> contributorAttributes;
public Contributor(String orcid, String creditName, String email, Set<ContributorAttribute> contributorAttributes) {
this.orcid = orcid;
this.creditName = creditName;
this.email = email;
this.contributorAttributes = contributorAttributes;
}
public String getOrcid() {
return orcid;
}
public void setOrcid(String orcid) {
this.orcid = orcid;
}
public String getCreditName() {
return creditName;
}
public void setCreditName(String creditName) {
this.creditName = creditName;
}
public String getEmail() {
return email;
}
public void setEmail(String email) {
this.email = email;
}
public Set<ContributorAttribute> getContributorAttributes() {
return contributorAttributes;
}
public void setContributorAttributes(Set<ContributorAttribute> contributorAttributes) {
this.contributorAttributes = contributorAttributes;
}
@Override
public String toString() {
return "Contributor{" +
"orcid='" + orcid + '\'' +
", creditName='" + creditName + '\'' +
", email='" + email + '\'' +
", contributorAttributes=" + contributorAttributes +
'}';
}
@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}
Contributor that = (Contributor) o;
if (contributorAttributes != null ? !contributorAttributes
.equals(that.contributorAttributes) : that.contributorAttributes != null) {
return false;
}
if (creditName != null ? !creditName.equals(that.creditName) : that.creditName != null) {
return false;
}
if (email != null ? !email.equals(that.email) : that.email != null) {
return false;
}
if (orcid != null ? !orcid.equals(that.orcid) : that.orcid != null) {
return false;
}
return true;
}
@Override
public int hashCode() {
int result = orcid != null ? orcid.hashCode() : 0;
result = 31 * result + (creditName != null ? creditName.hashCode() : 0);
result = 31 * result + (email != null ? email.hashCode() : 0);
result = 31 * result + (contributorAttributes != null ? contributorAttributes.hashCode() : 0);
return result;
}
}

78
dspace-api/src/main/java/org/dspace/authority/orcid/model/ContributorAttribute.java
View File

@@ -1,78 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
/**
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public class ContributorAttribute {
private ContributorAttributeRole role;
private ContributorAttributeSequence sequence;
public ContributorAttribute(ContributorAttributeRole role, ContributorAttributeSequence sequence) {
this.role = role;
this.sequence = sequence;
}
public ContributorAttributeRole getRole() {
return role;
}
public void setRole(ContributorAttributeRole role) {
this.role = role;
}
public ContributorAttributeSequence getSequence() {
return sequence;
}
public void setSequence(ContributorAttributeSequence sequence) {
this.sequence = sequence;
}
@Override
public String toString() {
return "ContributorAttribute{" +
"role=" + role +
", sequence=" + sequence +
'}';
}
@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}
ContributorAttribute that = (ContributorAttribute) o;
if (role != that.role) {
return false;
}
if (sequence != that.sequence) {
return false;
}
return true;
}
@Override
public int hashCode() {
int result = role != null ? role.hashCode() : 0;
result = 31 * result + (sequence != null ? sequence.hashCode() : 0);
return result;
}
}

32
dspace-api/src/main/java/org/dspace/authority/orcid/model/ContributorAttributeRole.java
View File

@@ -1,32 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
/**
* http://support.orcid.org/knowledgebase/articles/118843-anatomy-of-a-contributor
*
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public enum ContributorAttributeRole {
AUTHOR,
ASSIGNEE,
EDITOR,
CHAIR_OR_TRANSLATOR,
CO_INVESTIGATOR,
CO_INVENTOR,
GRADUATE_STUDENT,
OTHER_INVENTOR,
PRINCIPAL_INVESTIGATOR,
POSTDOCTORAL_RESEARCHER,
SUPPORT_STAFF
}

23
dspace-api/src/main/java/org/dspace/authority/orcid/model/ContributorAttributeSequence.java
View File

@@ -1,23 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
/**
* http://support.orcid.org/knowledgebase/articles/118843-anatomy-of-a-contributor
*
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public enum ContributorAttributeSequence {
FIRST,
ADDITIONAL
}

116
dspace-api/src/main/java/org/dspace/authority/orcid/model/Work.java
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@@ -1,116 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
import java.util.Set;
/**
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public class Work {
private WorkTitle workTitle;
private String description;
private Citation citation;
private WorkType workType;
private String publicationDate;
private WorkExternalIdentifier workExternalIdentifier;
private String url;
private Set<Contributor> contributors;
private String workSource;
public WorkTitle getWorkTitle() {
return workTitle;
}
public void setWorkTitle(WorkTitle workTitle) {
this.workTitle = workTitle;
}
public String getDescription() {
return description;
}
public void setDescription(String description) {
this.description = description;
}
public Citation getCitation() {
return citation;
}
public void setCitation(Citation citation) {
this.citation = citation;
}
public WorkType getWorkType() {
return workType;
}
public void setWorkType(WorkType workType) {
this.workType = workType;
}
public String getPublicationDate() {
return publicationDate;
}
public void setPublicationDate(String publicationDate) {
this.publicationDate = publicationDate;
}
public WorkExternalIdentifier getWorkExternalIdentifier() {
return workExternalIdentifier;
}
public void setWorkExternalIdentifier(WorkExternalIdentifier workExternalIdentifier) {
this.workExternalIdentifier = workExternalIdentifier;
}
public String getUrl() {
return url;
}
public void setUrl(String url) {
this.url = url;
}
public Set<Contributor> getContributors() {
return contributors;
}
public void setContributors(Set<Contributor> contributors) {
this.contributors = contributors;
}
public String getWorkSource() {
return workSource;
}
public void setWorkSource(String workSource) {
this.workSource = workSource;
}
@Override
public String toString() {
return "Work{" +
"workTitle=" + workTitle +
", description='" + description + '\'' +
", citation=" + citation +
", workType=" + workType +
", publicationDate='" + publicationDate + '\'' +
", workExternalIdentifier=" + workExternalIdentifier +
", url='" + url + '\'' +
", contributors=" + contributors +
", workSource='" + workSource + '\'' +
'}';
}
}

73
dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkExternalIdentifier.java
View File

@@ -1,73 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
/**
* http://support.orcid.org/knowledgebase/articles/118807
*
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public class WorkExternalIdentifier {
private WorkExternalIdentifierType workExternalIdentifierType;
private String workExternalIdenfitierID;
public WorkExternalIdentifier(WorkExternalIdentifierType workExternalIdentifierType,
String workExternalIdenfitierID) {
this.workExternalIdentifierType = workExternalIdentifierType;
this.workExternalIdenfitierID = workExternalIdenfitierID;
}
public WorkExternalIdentifierType getWorkExternalIdentifierType() {
return workExternalIdentifierType;
}
public void setWorkExternalIdentifierType(WorkExternalIdentifierType workExternalIdentifierType) {
this.workExternalIdentifierType = workExternalIdentifierType;
}
@Override
public String toString() {
return "WorkExternalIdentifier{" +
"workExternalIdentifierType=" + workExternalIdentifierType +
", workExternalIdenfitierID='" + workExternalIdenfitierID + '\'' +
'}';
}
@Override
public boolean equals(Object o) {
if (this == o) {
return true;
}
if (o == null || getClass() != o.getClass()) {
return false;
}
WorkExternalIdentifier that = (WorkExternalIdentifier) o;
if (workExternalIdenfitierID != null ? !workExternalIdenfitierID
.equals(that.workExternalIdenfitierID) : that.workExternalIdenfitierID != null) {
return false;
}
if (workExternalIdentifierType != that.workExternalIdentifierType) {
return false;
}
return true;
}
@Override
public int hashCode() {
int result = workExternalIdentifierType != null ? workExternalIdentifierType.hashCode() : 0;
result = 31 * result + (workExternalIdenfitierID != null ? workExternalIdenfitierID.hashCode() : 0);
return result;
}
}

42
dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkExternalIdentifierType.java
View File

@@ -1,42 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
/**
* http://support.orcid.org/knowledgebase/articles/118807
*
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public enum WorkExternalIdentifierType {
// OTHER_ID,
ARXIV,
ASIN,
ASIN_TLD,
BIBCODE,
DOI,
EID,
ISBN,
ISSN,
JFM,
JSTOR,
LCCN,
MR,
OCLC,
OL,
OSTI,
PMC,
PMID,
RFC,
SSRN,
ZBL
}

64
dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkTitle.java
View File

@@ -1,64 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
import java.util.Map;
/**
* http://support.orcid.org/knowledgebase/articles/118807
*
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public class WorkTitle {
private String title;
private String subtitle;
private Map<String, String> translatedTitles;
public WorkTitle(String title, String subtitle, Map<String, String> translatedTitles) {
this.title = title;
this.subtitle = subtitle;
this.translatedTitles = translatedTitles;
}
public String getTitle() {
return title;
}
public void setTitle(String title) {
this.title = title;
}
public String getSubtitle() {
return subtitle;
}
public void setSubtitle(String subtitle) {
this.subtitle = subtitle;
}
public String getTranslatedTitles(String languageCode) {
return translatedTitles.get(languageCode);
}
public void setTranslatedTitle(String languageCode, String translatedTitle) {
translatedTitles.put(languageCode, translatedTitle);
}
@Override
public String toString() {
return "WorkTitle{" +
"title='" + title + '\'' +
", subtitle='" + subtitle + '\'' +
", translatedTitles=" + translatedTitles +
'}';
}
}

57
dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkType.java
View File

@@ -1,57 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.model;
/**
* http://support.orcid.org/knowledgebase/articles/118795
*
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public enum WorkType {
BOOK,
BOOK_CHAPTER,
BOOK_REVIEW,
DICTIONARY_ENTRY,
DISSERTATION,
ENCYCLOPEDIA_ARTICLE,
EDITED_BOOK,
JOURNAL_ARTICLE,
JOURNAL_ISSUE,
MAGAZINE_ARTICLE,
MANUAL,
ONLINE_RESOURCE,
NEWSLETTER_ARTICLE,
NEWSPAPER_ARTICLE,
REPORT,
RESEARCH_TOOL,
SUPERVISED_STUDENT_PUBLICATION,
TEST,
TRANSLATION,
WEBSITE,
CONFERENCE_ABSTRACT,
CONFERENCE_PAPER,
CONFERENCE_POSTER,
DISCLOSURE,
LICENSE,
PATENT,
REGISTERED_COPYRIGHT,
ARTISTIC_PERFORMANCE,
DATA_SET,
INVENTION,
LECTURE_SPEECH,
RESEARCH_TECHNIQUE,
SPIN_OFF_COMPANY,
STANDARDS_AND_POLICY,
TECHNICAL_STANDARD,
OTHER
}

24
dspace-api/src/main/java/org/dspace/authority/orcid/xml/Converter.java
View File

@@ -7,8 +7,16 @@
*/
package org.dspace.authority.orcid.xml;
import java.io.InputStream;
import java.net.URISyntaxException;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller;
import org.apache.log4j.Logger;
import org.w3c.dom.Document;
import org.xml.sax.SAXException;
/**
* @param <T> type
@@ -24,11 +32,15 @@ public abstract class Converter<T> {
*/
private static Logger log = Logger.getLogger(Converter.class);
public abstract T convert(InputStream document);
protected void processError(Document xml) {
String errorMessage = XMLErrors.getErrorMessage(xml);
log.error("The orcid-message reports an error: " + errorMessage);
protected Object unmarshall(InputStream input, Class<?> type) throws SAXException, URISyntaxException {
try {
JAXBContext context = JAXBContext.newInstance(type);
Unmarshaller unmarshaller = context.createUnmarshaller();
return unmarshaller.unmarshal(input);
} catch (JAXBException e) {
throw new RuntimeException("Unable to unmarshall orcid message" + e);
}
}
public abstract T convert(Document document);
}

77
dspace-api/src/main/java/org/dspace/authority/orcid/xml/XMLErrors.java
View File

@@ -1,77 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.xml;
import javax.xml.xpath.XPathExpressionException;
import org.apache.log4j.Logger;
import org.dspace.authority.util.XMLUtils;
import org.w3c.dom.Document;
/**
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public class XMLErrors {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(XMLErrors.class);
private static final String ERROR_DESC = "/orcid-message/error-desc";
/**
* Default constructor
*/
private XMLErrors() { }
/**
* Evaluates whether a given xml document contains errors or not.
*
* @param xml The given xml document
* @return true if the given xml document is null
* or if it contains errors
*/
public static boolean check(Document xml) {
if (xml == null) {
return true;
}
String textContent = null;
try {
textContent = XMLUtils.getTextContent(xml, ERROR_DESC);
} catch (XPathExpressionException e) {
log.error("Error while checking for errors in orcid message", e);
}
return textContent == null;
}
public static String getErrorMessage(Document xml) {
if (xml == null) {
return "Did not receive an XML document.";
}
String textContent = null;
try {
textContent = XMLUtils.getTextContent(xml, ERROR_DESC);
} catch (XPathExpressionException e) {
log.error("Error while checking for errors in orcid message", e);
}
return textContent;
}
}

251
dspace-api/src/main/java/org/dspace/authority/orcid/xml/XMLtoBio.java
View File

@@ -7,20 +7,21 @@
*/
package org.dspace.authority.orcid.xml;
import java.io.InputStream;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import javax.xml.xpath.XPathExpressionException;
import org.apache.log4j.Logger;
import org.dspace.authority.orcid.model.Bio;
import org.dspace.authority.orcid.model.BioExternalIdentifier;
import org.dspace.authority.orcid.model.BioName;
import org.dspace.authority.orcid.model.BioResearcherUrl;
import org.dspace.authority.util.XMLUtils;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.dspace.authority.orcid.Orcidv2;
import org.dspace.utils.DSpace;
import org.orcid.jaxb.model.common_v2.OrcidId;
import org.orcid.jaxb.model.record_v2.Person;
import org.orcid.jaxb.model.search_v2.Result;
import org.orcid.jaxb.model.search_v2.Search;
import org.xml.sax.SAXException;
/**
* @author Antoine Snyers (antoine at atmire.com)
@@ -35,218 +36,38 @@ public class XMLtoBio extends Converter {
*/
private static Logger log = Logger.getLogger(XMLtoBio.class);
/**
* orcid-message XPATHs
*/
protected String ORCID_BIO = "//orcid-bio";
// protected String ORCID = "parent::*/orcid";
protected String ORCID = "parent::*/orcid-identifier/path";
protected String PERSONAL_DETAILS = "personal-details";
protected String GIVEN_NAMES = PERSONAL_DETAILS + "/given-names";
protected String FAMILY_NAME = PERSONAL_DETAILS + "/family-name";
protected String CREDIT_NAME = PERSONAL_DETAILS + "/credit-name";
protected String OTHER_NAMES = PERSONAL_DETAILS + "/other-names";
protected String OTHER_NAME = OTHER_NAMES + "/other-name";
protected String CONTACT_DETAILS = "contact-details";
protected String COUNTRY = CONTACT_DETAILS + "/address/country";
protected String KEYWORDS = "keywords";
protected String KEYWORD = KEYWORDS + "/keyword";
protected String EXTERNAL_IDENTIFIERS = "external-identifiers";
protected String EXTERNAL_IDENTIFIER = EXTERNAL_IDENTIFIERS + "/external-identifier";
protected String EXTERNAL_ID_ORCID = "external-id-orcid";
protected String EXTERNAL_ID_COMMNON_NAME = "external-id-common-name";
protected String EXTERNAL_ID_REFERENCE = "external-id-reference";
protected String EXTERNAL_ID_URL = "external-id-url";
protected String RESEARCHER_URLS = "researcher-urls";
protected String RESEARCHER_URL = "researcher-urls/researcher-url";
protected String URL_NAME = "url-name";
protected String URL = "url";
protected String BIOGRAPHY = ORCID_BIO + "/biography";
protected String AFFILIATIONS = ORCID_BIO + "/affiliation";
/**
* Regex
*/
protected String ORCID_NOT_FOUND = "ORCID [\\d-]* not found";
@Override
public List<Bio> convert(Document xml) {
List<Bio> result = new ArrayList<Bio>();
if (XMLErrors.check(xml)) {
public List<Person> convert(InputStream xml) {
List<Person> bios = new ArrayList<>();
try {
Iterator<Node> iterator = XMLUtils.getNodeListIterator(xml, ORCID_BIO);
while (iterator.hasNext()) {
Bio bio = convertBio(iterator.next());
result.add(bio);
Orcidv2 connector = new DSpace().getServiceManager().getServiceByName("AuthoritySource", Orcidv2.class);
Search search = (Search) unmarshall(xml, Search.class);
for (Result result : search.getResult()) {
OrcidId orcidIdentifier = result.getOrcidIdentifier();
if (orcidIdentifier != null) {
log.debug("Found OrcidId=" + orcidIdentifier.toString());
String orcid = orcidIdentifier.getUriPath();
Person bio = connector.getBio(orcid);
if (bio != null) {
bios.add(bio);
}
} catch (XPathExpressionException e) {
log.error("Error in xpath syntax", e);
}
} else {
processError(xml);
}
} catch (SAXException | URISyntaxException e) {
log.error(e);
}
return bios;
}
return result;
}
private Bio convertBio(Node node) {
Bio bio = new Bio();
setOrcid(node, bio);
setPersonalDetails(node, bio);
setContactDetails(node, bio);
setKeywords(node, bio);
setExternalIdentifiers(node, bio);
setResearcherUrls(node, bio);
setBiography(node, bio);
return bio;
}
@Override
protected void processError(Document xml) {
String errorMessage = XMLErrors.getErrorMessage(xml);
if (errorMessage.matches(ORCID_NOT_FOUND)) {
// do something?
}
log.error("The orcid-message reports an error: " + errorMessage);
}
private void setOrcid(Node node, Bio bio) {
public Person convertSinglePerson(InputStream xml) {
Person person = null;
try {
String orcid = XMLUtils.getTextContent(node, ORCID);
bio.setOrcid(orcid);
} catch (XPathExpressionException e) {
log.debug("Error in finding the biography in bio xml.", e);
person = (Person) unmarshall(xml, Person.class);
return person;
} catch (SAXException | URISyntaxException e) {
log.error(e);
}
return null;
}
protected void setBiography(Node xml, Bio bio) {
try {
String biography = XMLUtils.getTextContent(xml, BIOGRAPHY);
bio.setBiography(biography);
} catch (XPathExpressionException e) {
log.error("Error in finding the biography in bio xml.", e);
}
}
protected void setResearcherUrls(Node xml, Bio bio) {
try {
NodeList researcher_urls = XMLUtils.getNodeList(xml, RESEARCHER_URL);
if (researcher_urls != null) {
for (int i = 0; i < researcher_urls.getLength(); i++) {
Node researcher_url = researcher_urls.item(i);
if (researcher_url.getNodeType() != Node.TEXT_NODE) {
String url_name = XMLUtils.getTextContent(researcher_url, URL_NAME);
String url = XMLUtils.getTextContent(researcher_url, URL);
BioResearcherUrl researcherUrl = new BioResearcherUrl(url_name, url);
bio.addResearcherUrl(researcherUrl);
}
}
}
} catch (XPathExpressionException e) {
log.error("Error in finding the researcher url in bio xml.", e);
}
}
protected void setExternalIdentifiers(Node xml, Bio bio) {
try {
Iterator<Node> iterator = XMLUtils.getNodeListIterator(xml, EXTERNAL_IDENTIFIER);
while (iterator.hasNext()) {
Node external_identifier = iterator.next();
String id_orcid = XMLUtils.getTextContent(external_identifier, EXTERNAL_ID_ORCID);
String id_common_name = XMLUtils.getTextContent(external_identifier, EXTERNAL_ID_COMMNON_NAME);
String id_reference = XMLUtils.getTextContent(external_identifier, EXTERNAL_ID_REFERENCE);
String id_url = XMLUtils.getTextContent(external_identifier, EXTERNAL_ID_URL);
BioExternalIdentifier externalIdentifier = new BioExternalIdentifier(id_orcid, id_common_name,
id_reference, id_url);
bio.addExternalIdentifier(externalIdentifier);
}
} catch (XPathExpressionException e) {
log.error("Error in finding the external identifier in bio xml.", e);
}
}
protected void setKeywords(Node xml, Bio bio) {
try {
NodeList keywords = XMLUtils.getNodeList(xml, KEYWORD);
if (keywords != null) {
for (int i = 0; i < keywords.getLength(); i++) {
String keyword = keywords.item(i).getTextContent();
String[] split = keyword.split(",");
for (String k : split) {
bio.addKeyword(k.trim());
}
}
}
} catch (XPathExpressionException e) {
log.error("Error in finding the keywords in bio xml.", e);
}
}
protected void setContactDetails(Node xml, Bio bio) {
try {
String country = XMLUtils.getTextContent(xml, COUNTRY);
bio.setCountry(country);
} catch (XPathExpressionException e) {
log.error("Error in finding the country in bio xml.", e);
}
}
protected void setPersonalDetails(Node xml, Bio bio) {
BioName name = bio.getName();
try {
String givenNames = XMLUtils.getTextContent(xml, GIVEN_NAMES);
name.setGivenNames(givenNames);
} catch (XPathExpressionException e) {
log.error("Error in finding the given names in bio xml.", e);
}
try {
String familyName = XMLUtils.getTextContent(xml, FAMILY_NAME);
name.setFamilyName(familyName);
} catch (XPathExpressionException e) {
log.error("Error in finding the family name in bio xml.", e);
}
try {
String creditName = XMLUtils.getTextContent(xml, CREDIT_NAME);
name.setCreditName(creditName);
} catch (XPathExpressionException e) {
log.error("Error in finding the credit name in bio xml.", e);
}
try {
Iterator<Node> iterator = XMLUtils.getNodeListIterator(xml, OTHER_NAME);
while (iterator.hasNext()) {
Node otherName = iterator.next();
String textContent = otherName.getTextContent();
name.getOtherNames().add(textContent.trim());
}
} catch (XPathExpressionException e) {
log.error("Error in finding the other names in bio xml.", e);
}
}
}

257
dspace-api/src/main/java/org/dspace/authority/orcid/xml/XMLtoWork.java
View File

@@ -1,257 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.authority.orcid.xml;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import javax.xml.xpath.XPathExpressionException;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.dspace.authority.orcid.model.Citation;
import org.dspace.authority.orcid.model.CitationType;
import org.dspace.authority.orcid.model.Contributor;
import org.dspace.authority.orcid.model.ContributorAttribute;
import org.dspace.authority.orcid.model.ContributorAttributeRole;
import org.dspace.authority.orcid.model.ContributorAttributeSequence;
import org.dspace.authority.orcid.model.Work;
import org.dspace.authority.orcid.model.WorkExternalIdentifier;
import org.dspace.authority.orcid.model.WorkExternalIdentifierType;
import org.dspace.authority.orcid.model.WorkTitle;
import org.dspace.authority.orcid.model.WorkType;
import org.dspace.authority.util.EnumUtils;
import org.dspace.authority.util.XMLUtils;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
/**
* @author Antoine Snyers (antoine at atmire.com)
* @author Kevin Van de Velde (kevin at atmire dot com)
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public class XMLtoWork extends Converter {
/**
* log4j logger
*/
private static Logger log = Logger.getLogger(XMLtoWork.class);
/**
* orcid-message XPATHs
*/
protected String ORCID_WORKS = "//orcid-works";
protected String ORCID_WORK = ORCID_WORKS + "/orcid-work";
protected String WORK_TITLE = "work-title";
protected String TITLE = WORK_TITLE + "/title";
protected String SUBTITLE = WORK_TITLE + "/subtitle";
protected String TRANSLATED_TITLES = WORK_TITLE + "/translated-title";
protected String TRANSLATED_TITLES_LANGUAGE = "@language-code";
protected String SHORT_DESCRIPTION = "short-description";
protected String WORK_CITATION = "work-citation";
protected String CITATION_TYPE = WORK_CITATION + "/work-citation-type";
protected String CITATION = WORK_CITATION + "/citation";
protected String WORK_TYPE = "work-type";
protected String PUBLICATION_DATE = "publication-date";
protected String YEAR = PUBLICATION_DATE + "/year";
protected String MONTH = PUBLICATION_DATE + "/month";
protected String DAY = PUBLICATION_DATE + "/day";
protected String WORK_EXTERNAL_IDENTIFIERS = "work-external-identifiers";
protected String WORK_EXTERNAL_IDENTIFIER = WORK_EXTERNAL_IDENTIFIERS + "/work-external-identifier";
protected String WORK_EXTERNAL_IDENTIFIER_TYPE = "work-external-identifier-type";
protected String WORK_EXTERNAL_IDENTIFIER_ID = "work-external-identifier-id";
protected String URL = "url";
protected String WORK_CONTRIBUTOR = "work-contributors";
protected String CONTRIBUTOR = WORK_CONTRIBUTOR + "/contributor";
protected String CONTRIBUTOR_ORCID = "contributor-orcid";
protected String CREDIT_NAME = "credit-name";
protected String CONTRIBUTOR_EMAIL = "contributor-email";
protected String CONTRIBUTOR_ATTRIBUTES = "contributor-attributes";
protected String CONTRIBUTOR_SEQUENCE = "contributor-sequence";
protected String CONTRIBUTOR_ROLE = "contributor-role";
protected String WORK_SOURCE = "work-source";
@Override
public List<Work> convert(Document document) {
List<Work> result = new ArrayList<Work>();
if (XMLErrors.check(document)) {
try {
Iterator<Node> iterator = XMLUtils.getNodeListIterator(document, ORCID_WORK);
while (iterator.hasNext()) {
Work work = convertWork(iterator.next());
result.add(work);
}
} catch (XPathExpressionException e) {
log.error("Error in xpath syntax", e);
}
} else {
processError(document);
}
return result;
}
protected Work convertWork(Node node) throws XPathExpressionException {
Work work = new Work();
setTitle(node, work);
setDescription(node, work);
setCitation(node, work);
setWorkType(node, work);
setPublicationDate(node, work);
setExternalIdentifiers(node, work);
setUrl(node, work);
setContributors(node, work);
setWorkSource(node, work);
return work;
}
protected void setWorkSource(Node node, Work work) throws XPathExpressionException {
String workSource = XMLUtils.getTextContent(node, WORK_SOURCE);
work.setWorkSource(workSource);
}
protected void setContributors(Node node, Work work) throws XPathExpressionException {
Set<Contributor> contributors = new HashSet<Contributor>();
Iterator<Node> iterator = XMLUtils.getNodeListIterator(node, CONTRIBUTOR);
while (iterator.hasNext()) {
Node nextContributorNode = iterator.next();
String orcid = XMLUtils.getTextContent(nextContributorNode, CONTRIBUTOR_ORCID);
String creditName = XMLUtils.getTextContent(nextContributorNode, CREDIT_NAME);
String email = XMLUtils.getTextContent(nextContributorNode, CONTRIBUTOR_EMAIL);
Set<ContributorAttribute> contributorAttributes = new HashSet<ContributorAttribute>();
NodeList attributeNodes = XMLUtils.getNodeList(nextContributorNode, CONTRIBUTOR_ATTRIBUTES);
Iterator<Node> attributesIterator = XMLUtils.getNodeListIterator(attributeNodes);
while (attributesIterator.hasNext()) {
Node nextAttribute = attributesIterator.next();
String roleText = XMLUtils.getTextContent(nextAttribute, CONTRIBUTOR_ROLE);
ContributorAttributeRole role = EnumUtils.lookup(ContributorAttributeRole.class, roleText);
String sequenceText = XMLUtils.getTextContent(nextAttribute, CONTRIBUTOR_SEQUENCE);
ContributorAttributeSequence sequence = EnumUtils
.lookup(ContributorAttributeSequence.class, sequenceText);
ContributorAttribute attribute = new ContributorAttribute(role, sequence);
contributorAttributes.add(attribute);
}
Contributor contributor = new Contributor(orcid, creditName, email, contributorAttributes);
contributors.add(contributor);
}
work.setContributors(contributors);
}
protected void setUrl(Node node, Work work) throws XPathExpressionException {
String url = XMLUtils.getTextContent(node, URL);
work.setUrl(url);
}
protected void setExternalIdentifiers(Node node, Work work) throws XPathExpressionException {
Iterator<Node> iterator = XMLUtils.getNodeListIterator(node, WORK_EXTERNAL_IDENTIFIER);
while (iterator.hasNext()) {
Node work_external_identifier = iterator.next();
String typeText = XMLUtils.getTextContent(work_external_identifier, WORK_EXTERNAL_IDENTIFIER_TYPE);
WorkExternalIdentifierType type = EnumUtils.lookup(WorkExternalIdentifierType.class, typeText);
String id = XMLUtils.getTextContent(work_external_identifier, WORK_EXTERNAL_IDENTIFIER_ID);
WorkExternalIdentifier externalID = new WorkExternalIdentifier(type, id);
work.setWorkExternalIdentifier(externalID);
}
}
protected void setPublicationDate(Node node, Work work) throws XPathExpressionException {
String year = XMLUtils.getTextContent(node, YEAR);
String month = XMLUtils.getTextContent(node, MONTH);
String day = XMLUtils.getTextContent(node, DAY);
String publicationDate = year;
if (StringUtils.isNotBlank(month)) {
publicationDate += "-" + month;
if (StringUtils.isNotBlank(day)) {
publicationDate += "-" + day;
}
}
work.setPublicationDate(publicationDate);
}
protected void setWorkType(Node node, Work work) throws XPathExpressionException {
String workTypeText = XMLUtils.getTextContent(node, WORK_TYPE);
WorkType workType = EnumUtils.lookup(WorkType.class, workTypeText);
work.setWorkType(workType);
}
protected void setCitation(Node node, Work work) throws XPathExpressionException {
String typeText = XMLUtils.getTextContent(node, CITATION_TYPE);
CitationType type = EnumUtils.lookup(CitationType.class, typeText);
String citationtext = XMLUtils.getTextContent(node, CITATION);
Citation citation = new Citation(type, citationtext);
work.setCitation(citation);
}
protected void setDescription(Node node, Work work) throws XPathExpressionException {
String description = null;
description = XMLUtils.getTextContent(node, SHORT_DESCRIPTION);
work.setDescription(description);
}
protected void setTitle(Node node, Work work) throws XPathExpressionException {
String title = XMLUtils.getTextContent(node, TITLE);
String subtitle = XMLUtils.getTextContent(node, SUBTITLE);
Map<String, String> translatedTitles = new HashMap<String, String>();
NodeList nodeList = XMLUtils.getNodeList(node, TRANSLATED_TITLES);
Iterator<Node> iterator = XMLUtils.getNodeListIterator(nodeList);
while (iterator.hasNext()) {
Node languageNode = iterator.next();
String language = XMLUtils.getTextContent(languageNode, TRANSLATED_TITLES_LANGUAGE);
String translated_title = XMLUtils.getTextContent(languageNode, ".");
translatedTitles.put(language, translated_title);
}
WorkTitle workTitle = new WorkTitle(title, subtitle, translatedTitles);
work.setWorkTitle(workTitle);
}
}

15
dspace-api/src/main/java/org/dspace/authority/rest/RESTConnector.java
View File

@@ -10,13 +10,12 @@ package org.dspace.authority.rest;
import java.io.InputStream;
import java.util.Scanner;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.HttpResponse;
import org.apache.http.client.HttpClient;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.log4j.Logger;
import org.dspace.authority.util.XMLUtils;
import org.w3c.dom.Document;
/**
* @author Antoine Snyers (antoine at atmire.com)
@@ -37,26 +36,26 @@ public class RESTConnector {
this.url = url;
}
public Document get(String path) {
Document document = null;
public InputStream get(String path, String accessToken) {
InputStream result = null;
path = trimSlashes(path);
String fullPath = url + '/' + path;
HttpGet httpGet = new HttpGet(fullPath);
if (StringUtils.isNotBlank(accessToken)) {
httpGet.addHeader("Content-Type", "application/vnd.orcid+xml");
httpGet.addHeader("Authorization","Bearer " + accessToken);
}
try {
HttpClient httpClient = HttpClientBuilder.create().build();
HttpResponse getResponse = httpClient.execute(httpGet);
//do not close this httpClient
result = getResponse.getEntity().getContent();
document = XMLUtils.convertStreamToXML(result);
} catch (Exception e) {
getGotError(e, fullPath);
}
return document;
return result;
}
protected void getGotError(Exception e, String fullPath) {

10
dspace-api/src/main/java/org/dspace/authority/rest/RestSource.java
View File

@@ -7,9 +7,7 @@
*/
package org.dspace.authority.rest;
import java.util.List;
import org.dspace.authority.AuthorityValue;
import org.dspace.authority.SolrAuthorityInterface;
/**
* @author Antoine Snyers (antoine at atmire.com)
@@ -17,15 +15,11 @@ import org.dspace.authority.AuthorityValue;
* @author Ben Bosman (ben at atmire dot com)
* @author Mark Diggory (markd at atmire dot com)
*/
public abstract class RestSource {
public abstract class RestSource implements SolrAuthorityInterface {
protected RESTConnector restConnector;
public RestSource(String url) {
this.restConnector = new RESTConnector(url);
}
public abstract List<AuthorityValue> queryAuthorities(String text, int max);
public abstract AuthorityValue queryAuthorityID(String id);
}

7
dspace-api/src/main/java/org/dspace/content/authority/SolrAuthority.java
View File

@@ -21,8 +21,8 @@ import org.apache.solr.common.SolrDocumentList;
import org.apache.solr.common.params.CommonParams;
import org.dspace.authority.AuthoritySearchService;
import org.dspace.authority.AuthorityValue;
import org.dspace.authority.SolrAuthorityInterface;
import org.dspace.authority.factory.AuthorityServiceFactory;
import org.dspace.authority.rest.RestSource;
import org.dspace.authority.service.AuthorityValueService;
import org.dspace.content.Collection;
import org.dspace.core.ConfigurationManager;
@@ -37,8 +37,9 @@ import org.dspace.services.factory.DSpaceServicesFactory;
public class SolrAuthority implements ChoiceAuthority {
private static final Logger log = Logger.getLogger(SolrAuthority.class);
protected RestSource source = DSpaceServicesFactory.getInstance().getServiceManager()
.getServiceByName("AuthoritySource", RestSource.class);
protected SolrAuthorityInterface source =
DSpaceServicesFactory.getInstance().getServiceManager()
.getServiceByName("AuthoritySource", SolrAuthorityInterface.class);
protected boolean externalResults = false;
protected final AuthorityValueService authorityValueService = AuthorityServiceFactory.getInstance()
.getAuthorityValueService();

4
dspace/config/dspace.cfg
View File

@@ -1433,6 +1433,10 @@ sherpa.romeo.url = http://www.sherpa.ac.uk/romeo/api29.php
#plugin.named.org.dspace.content.authority.ChoiceAuthority = \
# org.dspace.content.authority.SolrAuthority = SolrAuthorAuthority
# URL of ORCID API
# Defaults to using the Public API (pub.orcid.org)
orcid.api.url = https://pub.orcid.org/v2.1
## The DCInputAuthority plugin is automatically configured with every
## value-pairs element in input-forms.xml, namely:
## common_identifiers, common_types, common_iso_languages

6
dspace/config/spring/api/orcid-authority-services.xml
View File

@@ -18,7 +18,7 @@
<bean name="AuthorityTypes" class="org.dspace.authority.AuthorityTypes">
<property name="types">
<list>
<bean class="org.dspace.authority.orcid.OrcidAuthorityValue"/>
<bean class="org.dspace.authority.orcid.Orcidv2AuthorityValue"/>
<bean class="org.dspace.authority.PersonAuthorityValue"/>
</list>
</property>
@@ -32,8 +32,8 @@
</bean>
<alias name="OrcidSource" alias="AuthoritySource"/>
<bean name="OrcidSource" class="org.dspace.authority.orcid.Orcid">
<constructor-arg value="http://pub.orcid.org"/>
<bean name="OrcidSource" class="org.dspace.authority.orcid.Orcidv2" init-method="init">
<constructor-arg value="${orcid.api.url}"/>
</bean>

15
pom.xml
View File

@@ -1658,6 +1658,21 @@
</repository>
</distributionManagement>
<!-- Enable access to artifacts in Sonatype's snapshot repo for Snapshots ONLY -->
<repositories>
<repository>
<id>maven-snapshots</id>
<url>http://oss.sonatype.org/content/repositories/snapshots</url>
<layout>default</layout>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>org.apache.poi</groupId>