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RDF: dates for ORCID record modifications
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@stain
stain committed May 28, 2013
1 parent 1a89cbb commit 1c8c576
Showing 1 changed file with 122 additions and 25 deletions.
147 changes: 122 additions & 25 deletions orcid-api-common/src/main/java/org/orcid/api/common/writer/rdf/RDFMessageBodyWriter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,6 @@
import static org.orcid.api.common.OrcidApiConstants.PROFILE_POST_PATH;
import static org.orcid.api.common.OrcidApiConstants.TEXT_N3;
import static org.orcid.api.common.OrcidApiConstants.TEXT_TURTLE;
import static org.orcid.api.common.OrcidApiConstants.WORKS_PATH;

import java.io.IOException;
import java.io.InputStream;
Expand All @@ -30,6 +29,7 @@
import java.lang.reflect.Type;
import java.net.URI;
import java.nio.charset.Charset;
import java.util.Arrays;
import java.util.List;

import javax.ws.rs.Produces;
Expand All @@ -41,29 +41,32 @@
import javax.ws.rs.core.UriInfo;
import javax.ws.rs.ext.MessageBodyWriter;
import javax.ws.rs.ext.Provider;
import javax.xml.datatype.XMLGregorianCalendar;

import org.orcid.api.common.OrcidApiService;
import org.orcid.jaxb.model.message.Address;
import org.orcid.jaxb.model.message.Biography;
import org.orcid.jaxb.model.message.ContactDetails;
import org.orcid.jaxb.model.message.CreationMethod;
import org.orcid.jaxb.model.message.Email;
import org.orcid.jaxb.model.message.ErrorDesc;
import org.orcid.jaxb.model.message.LastModifiedDate;
import org.orcid.jaxb.model.message.OrcidBio;
import org.orcid.jaxb.model.message.OrcidHistory;
import org.orcid.jaxb.model.message.OrcidMessage;
import org.orcid.jaxb.model.message.OrcidProfile;
import org.orcid.jaxb.model.message.PersonalDetails;
import org.orcid.jaxb.model.message.ResearcherUrl;
import org.orcid.jaxb.model.message.ResearcherUrls;
import org.springframework.beans.factory.annotation.Value;

import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
import com.hp.hpl.jena.datatypes.xsd.impl.XSDDateTimeType;
import com.hp.hpl.jena.ontology.DatatypeProperty;
import com.hp.hpl.jena.ontology.Individual;
import com.hp.hpl.jena.ontology.ObjectProperty;
import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.Ontology;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.ModelFactory;

/**
Expand All @@ -81,8 +84,8 @@ public class RDFMessageBodyWriter implements MessageBodyWriter<OrcidMessage> {
private static final String PAV = "http://purl.org/pav/";
private static final String PAV_RDF = "pav.rdf";
private static final String PROV_O_RDF = "prov-o.rdf";
private static final String PROV = "http://www.w3.org/prov#";
private static final String PROV_O = "http://www.w3.org/prov-o#";
private static final String PROV = "http://www.w3.org/ns/prov#";
private static final String PROV_O = "http://www.w3.org/ns/prov-o#";
private static final String FOAF_0_1 = "http://xmlns.com/foaf/0.1/";
protected static final String TMP_BASE = "app://614879b4-48c3-45ab-a828-2a72e43f80d9/";
private static final Charset UTF8 = Charset.forName("UTF-8");
Expand Down Expand Up @@ -114,14 +117,19 @@ public class RDFMessageBodyWriter implements MessageBodyWriter<OrcidMessage> {
private OntClass provAgent;
private ObjectProperty provWasAttributedTo;
private DatatypeProperty provGeneratedAt;
private ObjectProperty pavContributedBy;
private DatatypeProperty foafMbox;
private ObjectProperty pavCuratedBy;
private ObjectProperty foafMbox;
private ObjectProperty foafMaker;
private DatatypeProperty foafPlan;
private ObjectProperty foafPage;
private ObjectProperty foafHomepage;
private DatatypeProperty foafBasedNear;
private ObjectProperty foafBasedNear;
private DatatypeProperty pavLastUpdateAt;
private ObjectProperty provAlternateOf;
private ObjectProperty pavImportedBy;
private DatatypeProperty pavCreatedOn;
private DatatypeProperty provInvalidatedAt;
private DatatypeProperty pavContributedOn;


/**
Expand Down Expand Up @@ -270,13 +278,11 @@ private Individual describeAccount(OrcidProfile orcidProfile, OntModel m, Indivi
account.addProperty(foafPrimaryTopic, person);
OrcidHistory history = orcidProfile.getOrcidHistory();
if (history != null) {
if (orcidProfile.getOrcidHistory().isClaimed().booleanValue()) {
if (history.isClaimed().booleanValue()) {
// Set account as PersonalProfileDocument
account.addRDFType(foafPersonalProfileDocument);
account.addProperty(foafMaker, person);

// If it's claimed, he's probably done at least some contributions
account.addProperty(pavContributedBy, person);
}
// Who made the profile?
switch (history.getCreationMethod()) {
Expand All @@ -289,21 +295,33 @@ private Individual describeAccount(OrcidProfile orcidProfile, OntModel m, Indivi
break;
case API:
Individual api = m.createIndividual(MEMBER_API, provSoftwareAgent);
account.addProperty(pavCreatedWith, api);
account.addProperty(pavImportedBy, api);

if (history.isClaimed().booleanValue()) {
account.addProperty(pavCuratedBy, person);
}


break;
default:
// Some unknown agent!
account.addProperty(pavCreatedWith, m.createIndividual(null, provAgent));
}

if (history.getLastModifiedDate() != null) {
String time = history.getLastModifiedDate().getValue().toXMLFormat();
m.createTypedLiteral(time, XSDDatatype.XSDdateTime);
account.addLiteral(pavLastUpdateAt, time);

// Or does this work?
account.addLiteral(provGeneratedAt, history.getLastModifiedDate());

Literal when = calendarAsLiteral(history.getLastModifiedDate().getValue(), m);
account.addLiteral(pavLastUpdateAt, when);
account.addLiteral(provGeneratedAt, when);
}
if (history.getSubmissionDate() != null) {
account.addLiteral(pavCreatedOn,
calendarAsLiteral(history.getSubmissionDate().getValue(), m));
}
if (history.getCompletionDate() != null) {
account.addLiteral(pavContributedOn, calendarAsLiteral(history.getDeactivationDate().getValue(), m));
}
if (history.getDeactivationDate() != null) {
account.addLiteral(provInvalidatedAt, calendarAsLiteral(history.getDeactivationDate().getValue(), m));
}

}
Expand All @@ -317,6 +335,10 @@ private Individual describeAccount(OrcidProfile orcidProfile, OntModel m, Indivi
return account;
}

private Literal calendarAsLiteral(XMLGregorianCalendar cal, OntModel m) {
return m.createTypedLiteral(cal.toXMLFormat(), XSDDatatype.XSDdateTime);
}

private Individual describePerson(OrcidProfile orcidProfile, OntModel m) {
String orcidUri = orcidProfile.getOrcidId();
Individual person = m.createIndividual(orcidUri, foafPerson);
Expand All @@ -333,10 +355,57 @@ private Individual describePerson(OrcidProfile orcidProfile, OntModel m) {
describePersonalDetails(orcidBio.getPersonalDetails(), person, m);
describeContactDetails(orcidBio.getContactDetails(), person, m);
describeBiography(orcidBio.getBiography(), person, m);

describeResearcherUrls(orcidBio.getResearcherUrls(), person, m);
return person;
}

private void describeResearcherUrls(ResearcherUrls researcherUrls, Individual person, OntModel m) {
if (researcherUrls == null || researcherUrls.getResearcherUrl() == null) {
return;
}
for (ResearcherUrl url : researcherUrls.getResearcherUrl()) {
Individual page = m.createIndividual(url.getUrl().getValue(), null);
if (isHomePage(url)) {
person.addProperty(foafHomepage, page);
} else if(isFoaf(url)) {
// TODO: Is this the proper way to link to other FOAF URIs?
// What if we want to link to the URL of the other FOAF *Profile*?

// Note: We don't dear to do owl:sameAs or prov:specializationOf
// as we don't know the extent of the other FOAF profile - we'll
// suffice to say it's an alternate view of the same person
person.addProperty(provAlternateOf, page);
page.addRDFType(foafPerson);
page.addRDFType(provPerson);
person.addSeeAlso(page);
} else {
person.addProperty(foafPage, page);
}
}
}

private boolean isFoaf(ResearcherUrl url) {
if (url.getUrlName() == null || url.getUrlName().getContent() == null) {
return false;
}
return url.getUrlName().getContent().equalsIgnoreCase("foaf");
}

/**
* There's no indication in ORCID if the URL is a homepage or some other
* page, so we'll guess based on it's name, it be something similar to
* "home page".
*/
private boolean isHomePage(ResearcherUrl url) {
if (url.getUrlName() == null || url.getUrlName().getContent() == null) {
return false;
}
String name = url.getUrlName().getContent().toLowerCase();
List<String> candidates = Arrays.asList("homepage", "home", "home page", "personal",
"personal homepage", "personal home page");
return candidates.contains(name);
}

private void describeBiography(Biography biography, Individual person, OntModel m) {
if (biography != null) {
// FIXME: Which language is the biography written in? Can't assume EN
Expand All @@ -353,7 +422,9 @@ private void describeContactDetails(ContactDetails contactDetails, Individual pe
if (emails != null) {
for (Email email : emails) {
if (email.isCurrent()) {
person.addProperty(foafMbox, email.getValue());

Individual mbox = m.createIndividual("mailto:" + email.getValue(), null);
person.addProperty(foafMbox, mbox);
}
}
}
Expand Down Expand Up @@ -413,6 +484,8 @@ protected OntModel getOntModel() {

OntModel ontModel = ModelFactory.createOntologyModel();
ontModel.setNsPrefix("foaf", FOAF_0_1);
ontModel.setNsPrefix("prov", PROV);
ontModel.setNsPrefix("pav", PAV);
//ontModel.getDocumentManager().loadImports(foaf.getOntModel());
return ontModel;
}
Expand All @@ -424,13 +497,30 @@ protected synchronized void loadPav() {
OntModel ontModel = loadOntologyFromClasspath(PAV_RDF, PAV);

pavCreatedBy = ontModel.getObjectProperty(PAV + "createdBy");
pavContributedBy = ontModel.getObjectProperty(PAV + "contributedBy");
pavCuratedBy = ontModel.getObjectProperty(PAV + "curatedBy");
pavImportedBy = ontModel.getObjectProperty(PAV + "importedBy");
pavCreatedWith = ontModel.getObjectProperty(PAV + "createdWith");

pavLastUpdateAt = ontModel.getDatatypeProperty(PAV + "lastUpdateAt");
pavCreatedOn = ontModel.getDatatypeProperty(PAV + "createdOn");
pavLastUpdateAt = ontModel.getDatatypeProperty(PAV + "lastUpdateOn");
pavContributedOn = ontModel.getDatatypeProperty(PAV + "contributedOn");

checkNotNull(pavCreatedBy, pavCuratedBy, pavImportedBy, pavCreatedWith,
pavCreatedOn, pavLastUpdateAt, pavContributedOn);
pav = ontModel;
}

private void checkNotNull(Object... possiblyNulls) {
int i=0;
for (Object check : possiblyNulls) {
if (check == null) {
throw new IllegalStateException("Could not load item #" + i);
}
i++;
}

}

protected synchronized void loadProv() {
if (prov != null) {
return;
Expand All @@ -441,8 +531,11 @@ protected synchronized void loadProv() {
provAgent = ontModel.getOntClass(PROV + "Agent");
provSoftwareAgent = ontModel.getOntClass(PROV + "SoftwareAgent");
provWasAttributedTo = ontModel.getObjectProperty(PROV + "wasAttributedTo");
provAlternateOf = ontModel.getObjectProperty(PROV + "alternateOf");
provGeneratedAt = ontModel.getDatatypeProperty(PROV + "generatedAtTime");
provInvalidatedAt = ontModel.getDatatypeProperty(PROV + "invalidatedAtTime");

checkNotNull(provPerson, provAgent, provSoftwareAgent, provWasAttributedTo, provAlternateOf, provGeneratedAt, provInvalidatedAt);
prov = ontModel;
}

Expand Down Expand Up @@ -479,8 +572,8 @@ protected synchronized void loadFoaf() {
foafFamilyName = ontModel.getDatatypeProperty(FOAF_0_1 + "familyName");
foafAccountName = ontModel.getDatatypeProperty(FOAF_0_1 + "accountName");
foafPlan = ontModel.getDatatypeProperty(FOAF_0_1 + "plan");
foafMbox = ontModel.getDatatypeProperty(FOAF_0_1 + "mbox");
foafBasedNear = ontModel.getDatatypeProperty(FOAF_0_1 + "based_near");
foafMbox = ontModel.getObjectProperty(FOAF_0_1 + "mbox");
foafBasedNear = ontModel.getObjectProperty(FOAF_0_1 + "based_near");


foafPrimaryTopic = ontModel.getObjectProperty(FOAF_0_1 + "primaryTopic");
Expand All @@ -492,6 +585,10 @@ protected synchronized void loadFoaf() {
foafAccount = ontModel.getObjectProperty(FOAF_0_1 + "account");
foafAccountServiceHomepage = ontModel.getObjectProperty(FOAF_0_1 + "accountServiceHomepage");

checkNotNull(foafPerson,foafOnlineAccount,foafPersonalProfileDocument, foafName, foafGivenName, foafFamilyName, foafAccountName,
foafPlan, foafMbox, foafBasedNear, foafPrimaryTopic, foafMaker, foafPage, foafHomepage, foafPublications, foafAccount,
foafAccountServiceHomepage);

foaf = ontModel;
}

Expand Down

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