@Override
protected Protocol convert(File directory) {
Protocol protocol = new Protocol();
protocol.setIdentifier(directory.getName());
if (key != null) {}
return protocol;
}
@Override
public Resource objectToJena(Model toAddTo, Protocol protocol) throws IllegalArgumentException {
if (protocol.getResourceURL() == null) {
throw new IllegalArgumentException(String.format(msg_ResourceWithoutURI, "protocols"));
}
Resource res = toAddTo.createResource(protocol.getResourceURL().toString());
toAddTo.add(res, RDF.type, TOXBANK.PROTOCOL);
if (protocol.isSearchable() != null)
res.addLiteral(TOXBANK.ISSUMMARYSEARCHABLE, protocol.isSearchable());
res.addLiteral(TOXBANK.HASVERSIONINFO, protocol.getVersion());
if (protocol.getTitle() != null) res.addLiteral(DCTerms.title, protocol.getTitle());
if (protocol.getTimeModified() != null)
res.addLiteral(DCTerms.modified, protocol.getTimeModified());
if (protocol.getSubmissionDate() != null)
res.addLiteral(DCTerms.dateSubmitted, protocol.getSubmissionDate());
if (protocol.isPublished() != null) res.addLiteral(TOXBANK.ISPUBLISHED, protocol.isPublished());
if (protocol.getStatus() != null)
res.addLiteral(TOXBANK.HASSTATUS, protocol.getStatus().name());
if (protocol.getIdentifier() != null)
res.addLiteral(DCTerms.identifier, protocol.getIdentifier());
if (protocol.getAbstract() != null)
res.addLiteral(TOXBANK.HASABSTRACT, cleanLiteral(protocol.getAbstract()));
List<String> keywords = protocol.getKeywords();
if (keywords != null) {
for (String keyword : keywords) res.addLiteral(TOXBANK.HASKEYWORD, keyword);
}
if (protocol.getProjects() != null)
for (Project aproject : protocol.getProjects()) {
if (aproject.getResourceURL() == null)
throw new IllegalArgumentException(
String.format(msg_InvalidURI, "project", res.getURI()));
Resource project = projectIO.objectToJena(toAddTo, aproject);
res.addProperty(TOXBANK.HASPROJECT, project);
}
if (protocol.getOrganisation() != null) {
if (protocol.getOrganisation().getResourceURL() == null)
throw new IllegalArgumentException(
String.format(msg_InvalidURI, "organisation", res.getURI()));
Resource org = organisationIO.objectToJena(toAddTo, protocol.getOrganisation());
res.addProperty(TOXBANK.HASORGANISATION, org);
}
if (protocol.getOwner() != null) {
if (protocol.getOwner().getResourceURL() == null)
throw new IllegalArgumentException(
String.format(msg_InvalidURI, "protocol owner", res.getURI()));
Resource ownerRes = toAddTo.createResource(protocol.getOwner().getResourceURL().toString());
res.addProperty(TOXBANK.HASOWNER, ownerRes);
}
ToxBankResourceSet<User> authors = protocol.getAuthors();
if (authors != null)
for (User author : authors) {
if (author.getResourceURL() == null)
throw new IllegalArgumentException(String.format(msg_InvalidURI, "author", res.getURI()));
Resource user = userIO.objectToJena(toAddTo, author);
res.addProperty(TOXBANK.HASAUTHOR, user);
}
if (protocol.getDocument() != null) {
if (protocol.getDocument().getResourceURL() == null)
throw new IllegalArgumentException(String.format(msg_InvalidURI, "document", res.getURI()));
Resource documentRes =
toAddTo.createResource(protocol.getDocument().getResourceURL().toString());
res.addProperty(TOXBANK.HASDOCUMENT, documentRes);
}
if (protocol.getDataTemplate() != null) {
if (protocol.getDataTemplate().getResourceURL() == null)
throw new IllegalArgumentException(
String.format(msg_InvalidURI, "data template", res.getURI()));
Resource templateRes =
toAddTo.createResource(protocol.getDataTemplate().getResourceURL().toString());
res.addProperty(TOXBANK.HASTEMPLATE, templateRes);
}
if (protocol.getLicense() != null) {
toAddTo.add(res, DCTerms.license, toAddTo.createResource(protocol.getLicense().toString()));
}
return res;
}
@Override
public Protocol fromJena(Model source, Resource res) throws IllegalArgumentException {
Protocol protocol = new Protocol();
try {
protocol.setResourceURL(new URL(res.getURI()));
} catch (MalformedURLException e) {
throw new IllegalArgumentException(String.format(msg_InvalidURI, "protocol", res.getURI()));
}
try {
protocol.setSearchable(res.getProperty(TOXBANK.ISSUMMARYSEARCHABLE).getBoolean());
} catch (Exception x) {
protocol.setSearchable(false);
}
try {
protocol.setVersion(res.getProperty(TOXBANK.HASVERSIONINFO).getInt());
} catch (Exception x) {
protocol.setVersion(0);
}
try {
protocol.setPublished(res.getProperty(TOXBANK.ISPUBLISHED).getBoolean());
} catch (Exception x) {
protocol.setPublished(null);
}
try {
protocol.setTimeModified(res.getProperty(DCTerms.modified).getLong());
} catch (Exception x) {
protocol.setTimeModified(null);
}
try {
protocol.setSubmissionDate(res.getProperty(DCTerms.dateSubmitted).getLong());
} catch (Exception x) {
protocol.setSubmissionDate(null);
}
if (res.getProperty(DCTerms.title) != null)
protocol.setTitle(res.getProperty(DCTerms.title).getString());
if (res.getProperty(TOXBANK.HASSTATUS) != null)
try {
protocol.setStatus(Protocol.STATUS.valueOf(res.getProperty(TOXBANK.HASSTATUS).getString()));
} catch (Exception x) {
protocol.setStatus(STATUS.RESEARCH);
}
if (res.getProperty(DCTerms.identifier) != null)
protocol.setIdentifier(res.getProperty(DCTerms.identifier).getString());
if (res.getProperty(TOXBANK.HASABSTRACT) != null)
protocol.setAbstract(res.getProperty(TOXBANK.HASABSTRACT).getString());
StmtIterator keywords = res.listProperties(TOXBANK.HASKEYWORD);
while (keywords.hasNext()) {
protocol.addKeyword(keywords.next().getString());
}
String uri = null;
StmtIterator authors = res.listProperties(TOXBANK.HASAUTHOR);
while (authors.hasNext()) {
Resource authorRes = authors.next().getResource();
User author = userIO.fromJena(source, authorRes);
protocol.addAuthor(author);
}
authors.close();
StmtIterator projects = res.listProperties(TOXBANK.HASPROJECT);
while (projects.hasNext()) {
Resource projectRes = projects.next().getResource();
Project project = projectIO.fromJena(source, projectRes);
protocol.addProject(project);
}
projects.close();
if (res.getProperty(TOXBANK.HASORGANISATION) != null) {
Organisation org =
organisationIO.fromJena(source, res.getProperty(TOXBANK.HASORGANISATION).getResource());
protocol.setOrganisation(org);
}
if (res.getProperty(TOXBANK.HASOWNER) != null)
try {
uri = res.getProperty(TOXBANK.HASOWNER).getResource().getURI();
User author = new User();
author.setResourceURL(new URL(uri));
protocol.setOwner(author);
} catch (MalformedURLException e) {
throw new IllegalArgumentException(String.format(msg_InvalidURI, "a protocol owner", uri));
}
if (res.getProperty(TOXBANK.HASDOCUMENT) != null)
try {
uri = res.getProperty(TOXBANK.HASDOCUMENT).getResource().getURI();
Document document = new Document(new URL(uri));
protocol.setDocument(document);
} catch (MalformedURLException e) {
throw new IllegalArgumentException(String.format(msg_InvalidURI, "a document", uri));
}
if (res.getProperty(TOXBANK.HASTEMPLATE) != null)
try {
uri = res.getProperty(TOXBANK.HASTEMPLATE).getResource().getURI();
Template dataTemplate = new Template(new URL(uri));
protocol.setDataTemplate(dataTemplate);
} catch (MalformedURLException e) {
throw new IllegalArgumentException(String.format(msg_InvalidURI, "data template", uri));
}
if (res.getProperty(DCTerms.license) != null)
try {
protocol.setLicense(new URL(res.getProperty(DCTerms.license).getObject().toString()));
} catch (MalformedURLException e) {
throw new IllegalArgumentException(
String.format(
msg_InvalidURI, "a license", res.getProperty(DCTerms.license).getObject()));
}
return protocol;
}