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egonwegonw
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Updated RDF4J to 4.0.0
1 parent 4602a96 commit 51210df

35 files changed

Lines changed: 472 additions & 470 deletions

‎org.bridgedb.rdf/src/org/bridgedb/rdf/BridgeDBRdfHandler.java‎

Lines changed: 19 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -47,9 +47,7 @@
4747
import org.eclipse.rdf4j.model.Resource;
4848
import org.eclipse.rdf4j.model.Statement;
4949
import org.eclipse.rdf4j.model.Value;
50-
import org.eclipse.rdf4j.model.impl.BooleanLiteralImpl;
51-
import org.eclipse.rdf4j.model.impl.LiteralImpl;
52-
import org.eclipse.rdf4j.model.impl.URIImpl;
50+
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
5351
import org.eclipse.rdf4j.repository.Repository;
5452
import org.eclipse.rdf4j.repository.RepositoryConnection;
5553
import org.eclipse.rdf4j.repository.RepositoryException;
@@ -86,7 +84,7 @@ private void doParseRdfInputStream(InputStream stream) throws BridgeDBException
8684
RepositoryConnection repositoryConnection = null;
8785
try {
8886
repository = new SailRepository(new MemoryStore());
89-
repository.initialize();
87+
repository.init();
9088
repositoryConnection = repository.getConnection();
9189
repositoryConnection.add(stream, DEFAULT_BASE_URI, DEFAULT_FILE_FORMAT);
9290
readAllDataSources(repositoryConnection);
@@ -216,7 +214,7 @@ public DataSource readDataSource(RepositoryConnection repositoryConnection, Reso
216214

217215
private void readCodeMapper(RepositoryConnection repositoryConnection, String systemCode, Pattern regex) throws RepositoryException, BridgeDBException {
218216
RepositoryResult<Statement> statements =
219-
repositoryConnection.getStatements(null, BridgeDBConstants.SYSTEM_CODE_URI, new LiteralImpl(systemCode), true);
217+
repositoryConnection.getStatements(null, BridgeDBConstants.SYSTEM_CODE_URI, SimpleValueFactory.getInstance().createLiteral(systemCode), true);
220218
// String xrefPrefix = null;
221219
Resource codeMapperReseource = null;
222220
while (statements.hasNext()) {
@@ -321,7 +319,7 @@ public static void writeRdfToFile(File file, SortedSet<DataSource> dataSources)
321319
RepositoryConnection repositoryConnection = null;
322320
try {
323321
repository = new SailRepository(new MemoryStore());
324-
repository.initialize();
322+
repository.init();
325323
repositoryConnection = repository.getConnection();
326324
for (DataSource dataSource: dataSources){
327325
writeDataSource(repositoryConnection, dataSource);
@@ -341,29 +339,25 @@ private static void writeDataSource(RepositoryConnection repositoryConnection, D
341339
repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.DATA_SOURCE_URI);
342340

343341
if (dataSource.getFullName() != null){
344-
repositoryConnection.add(id, BridgeDBConstants.FULL_NAME_URI, new LiteralImpl(dataSource.getFullName()));
342+
repositoryConnection.add(id, BridgeDBConstants.FULL_NAME_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getFullName()));
345343
}
346344

347345
if (dataSource.getSystemCode() != null && (!dataSource.getSystemCode().trim().isEmpty())){
348-
repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, new LiteralImpl(dataSource.getSystemCode()));
346+
repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getSystemCode()));
349347
}
350348

351349
if (dataSource.getMainUrl() != null){
352-
repositoryConnection.add(id, BridgeDBConstants.MAIN_URL_URI, new LiteralImpl(dataSource.getMainUrl()));
350+
repositoryConnection.add(id, BridgeDBConstants.MAIN_URL_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getMainUrl()));
353351
}
354352

355353
if (dataSource.getExample() != null && dataSource.getExample().getId() != null){
356-
repositoryConnection.add(id, BridgeDBConstants.ID_EXAMPLE_URI, new LiteralImpl(dataSource.getExample().getId()));
354+
repositoryConnection.add(id, BridgeDBConstants.ID_EXAMPLE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getExample().getId()));
357355
}
358356

359-
if (dataSource.isPrimary()){
360-
repositoryConnection.add(id, BridgeDBConstants.PRIMARY_URI, BooleanLiteralImpl.TRUE);
361-
} else {
362-
repositoryConnection.add(id, BridgeDBConstants.PRIMARY_URI, BooleanLiteralImpl.FALSE);
363-
}
357+
repositoryConnection.add(id, BridgeDBConstants.PRIMARY_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.isPrimary()));
364358

365359
if (dataSource.getType() != null){
366-
repositoryConnection.add(id, BridgeDBConstants.TYPE_URI, new LiteralImpl(dataSource.getType()));
360+
repositoryConnection.add(id, BridgeDBConstants.TYPE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getType()));
367361
}
368362

369363
Pattern regex = DataSourcePatterns.getPatterns().get(dataSource);
@@ -391,16 +385,16 @@ private static void writeDataSource(RepositoryConnection repositoryConnection, D
391385

392386
Pattern pattern = DataSourcePatterns.getPatterns().get(dataSource);
393387
if (pattern != null && !pattern.toString().isEmpty()){
394-
Value patternValue = new LiteralImpl(pattern.toString());
388+
Value patternValue = SimpleValueFactory.getInstance().createLiteral(pattern.toString());
395389
repositoryConnection.add(id, BridgeDBConstants.HAS_REGEX_PATTERN_URI, patternValue);
396390
}
397391

398392
if (dataSource.getAlternative() != null){
399-
repositoryConnection.add(id, DCTermsConstants.ALTERNATIVE_URI, new LiteralImpl(dataSource.getAlternative()));
393+
repositoryConnection.add(id, DCTermsConstants.ALTERNATIVE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getAlternative()));
400394
}
401395

402396
if (dataSource.getDescription() != null){
403-
repositoryConnection.add(id, DCatConstants.DESCRIPTION_URI, new LiteralImpl(dataSource.getDescription()));
397+
repositoryConnection.add(id, DCatConstants.DESCRIPTION_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getDescription()));
404398
}
405399

406400
SortedSet<UriPattern> sortedPatterns = UriPattern.byCodeAndType(dataSource.getSystemCode(), UriPatternType.dataSourceUriPattern);
@@ -421,8 +415,8 @@ private static void writeCodeMapper(RepositoryConnection repositoryConnection, D
421415
}
422416
Resource id = asCodeMapperResource(dataSource);
423417
repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.CODE_MAPPER_URI);
424-
repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, new LiteralImpl(dataSource.getSystemCode()));
425-
Value prefixValue = new LiteralImpl(xrefPrefix);
418+
repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getSystemCode()));
419+
Value prefixValue = SimpleValueFactory.getInstance().createLiteral(xrefPrefix);
426420
repositoryConnection.add(id, BridgeDBConstants.XREF_PREFIX_URI, prefixValue);
427421

428422
SortedSet<UriPattern> sortedPatterns = UriPattern.byCodeAndType(dataSource.getSystemCode(), UriPatternType.codeMapperPattern);
@@ -476,17 +470,17 @@ private static RDFFormat getFormat(File file){
476470

477471
protected static Resource asResource(DataSource dataSource) {
478472
if (dataSource.getFullName() == null){
479-
return new URIImpl(BridgeDBConstants.DATA_SOURCE1 + "_bysysCode_" + scrub(dataSource.getSystemCode()));
473+
return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.DATA_SOURCE1 + "_bysysCode_" + scrub(dataSource.getSystemCode()));
480474
} else {
481-
return new URIImpl(BridgeDBConstants.DATA_SOURCE1 + "_" + scrub(dataSource.getFullName()));
475+
return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.DATA_SOURCE1 + "_" + scrub(dataSource.getFullName()));
482476
}
483477
}
484478

485479
protected static Resource asCodeMapperResource(DataSource dataSource) {
486480
if (dataSource.getFullName() == null){
487-
return new URIImpl(BridgeDBConstants.CODE_MAPPER1 + "_bysysCode_" + scrub(dataSource.getSystemCode()));
481+
return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.CODE_MAPPER1 + "_bysysCode_" + scrub(dataSource.getSystemCode()));
488482
} else {
489-
return new URIImpl(BridgeDBConstants.CODE_MAPPER1 + "_" + scrub(dataSource.getFullName()));
483+
return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.CODE_MAPPER1 + "_" + scrub(dataSource.getFullName()));
490484
}
491485
}
492486

‎org.bridgedb.rdf/src/org/bridgedb/rdf/OrganismRdf.java‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -22,16 +22,16 @@
2222
import java.io.IOException;
2323
import java.util.HashMap;
2424
import java.util.Set;
25+
2526
import org.bridgedb.bio.Organism;
2627
import org.bridgedb.rdf.constants.BridgeDBConstants;
2728
import org.bridgedb.rdf.constants.RdfConstants;
2829
import org.bridgedb.utils.BridgeDBException;
30+
import org.eclipse.rdf4j.model.IRI;
2931
import org.eclipse.rdf4j.model.Resource;
3032
import org.eclipse.rdf4j.model.Statement;
31-
import org.eclipse.rdf4j.model.URI;
3233
import org.eclipse.rdf4j.model.Value;
33-
import org.eclipse.rdf4j.model.impl.LiteralImpl;
34-
import org.eclipse.rdf4j.model.impl.URIImpl;
34+
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
3535
import org.eclipse.rdf4j.repository.RepositoryConnection;
3636
import org.eclipse.rdf4j.repository.RepositoryException;
3737
import org.eclipse.rdf4j.rio.RDFHandler;
@@ -64,8 +64,8 @@ public static final String getRdfLabel(Organism organism) {
6464
return scrub(organism.code());
6565
}
6666

67-
public static final URI getResourceId(Organism organism){
68-
return new URIImpl(BridgeDBConstants.ORGANISM1 + "_" + getRdfLabel(organism));
67+
public static final IRI getResourceId(Organism organism){
68+
return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.ORGANISM1 + "_" + getRdfLabel(organism));
6969
}
7070

7171
public static void addAll(RepositoryConnection repositoryConnection) throws IOException, RepositoryException {
@@ -82,11 +82,11 @@ public void addComments(RDFHandler handler) throws RDFHandlerException{
8282

8383
public static void add(RepositoryConnection repositoryConnection, Organism organism)
8484
throws IOException, RepositoryException {
85-
URI id = getResourceId(organism);
85+
IRI id = getResourceId(organism);
8686
repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.ORGANISM_URI);
87-
repositoryConnection.add(id, BridgeDBConstants.CODE_URI, new LiteralImpl(organism.code()));
88-
repositoryConnection.add(id, BridgeDBConstants.SHORT_NAME_URI, new LiteralImpl(organism.shortName()));
89-
repositoryConnection.add(id, BridgeDBConstants.LATIN_NAME_URI, new LiteralImpl(organism.latinName()));
87+
repositoryConnection.add(id, BridgeDBConstants.CODE_URI, SimpleValueFactory.getInstance().createLiteral(organism.code()));
88+
repositoryConnection.add(id, BridgeDBConstants.SHORT_NAME_URI, SimpleValueFactory.getInstance().createLiteral(organism.shortName()));
89+
repositoryConnection.add(id, BridgeDBConstants.LATIN_NAME_URI, SimpleValueFactory.getInstance().createLiteral(organism.latinName()));
9090
}
9191

9292
public static Object readRdf(Resource organismId, Set<Statement> allStatements) throws BridgeDBException {

‎org.bridgedb.rdf/src/org/bridgedb/rdf/RdfBase.java‎

Lines changed: 10 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -21,13 +21,14 @@
2121

2222
import java.util.HashSet;
2323
import java.util.Set;
24+
2425
import org.apache.log4j.Logger;
2526
import org.bridgedb.utils.BridgeDBException;
27+
import org.eclipse.rdf4j.model.IRI;
2628
import org.eclipse.rdf4j.model.Resource;
2729
import org.eclipse.rdf4j.model.Statement;
28-
import org.eclipse.rdf4j.model.URI;
2930
import org.eclipse.rdf4j.model.Value;
30-
import org.eclipse.rdf4j.model.impl.URIImpl;
31+
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
3132
import org.eclipse.rdf4j.repository.Repository;
3233
import org.eclipse.rdf4j.repository.RepositoryConnection;
3334
import org.eclipse.rdf4j.repository.RepositoryException;
@@ -61,7 +62,7 @@ static String convertToShortName(Value value) {
6162
return id;
6263
}
6364

64-
public static String getSingletonString(RepositoryConnection repositoryConnection, Resource id, URI predicate)
65+
public static String getSingletonString(RepositoryConnection repositoryConnection, Resource id, IRI predicate)
6566
throws BridgeDBException, RepositoryException {
6667
String result = getPossibleSingletonString(repositoryConnection, id, predicate);
6768
if (result == null){
@@ -71,7 +72,7 @@ public static String getSingletonString(RepositoryConnection repositoryConnectio
7172
}
7273

7374
public static String getPossibleSingletonString(RepositoryConnection repositoryConnection, Resource id,
74-
URI predicate) throws RepositoryException, BridgeDBException {
75+
IRI predicate) throws RepositoryException, BridgeDBException {
7576
Value result = getPossibleSingleton(repositoryConnection, id, predicate);
7677
if (result == null) {
7778
return null;
@@ -81,7 +82,7 @@ public static String getPossibleSingletonString(RepositoryConnection repositoryC
8182
}
8283

8384
static Resource getPossibleSingletonResource(RepositoryConnection repositoryConnection, Resource id,
84-
URI predicate) throws RepositoryException, BridgeDBException {
85+
IRI predicate) throws RepositoryException, BridgeDBException {
8586
Value value = getPossibleSingleton(repositoryConnection, id, predicate);
8687
return toResource(value);
8788
}
@@ -92,11 +93,11 @@ private static Resource toResource(Value value){
9293
} else if (value instanceof Resource){
9394
return (Resource)value;
9495
}
95-
return new URIImpl(value.stringValue());
96+
return SimpleValueFactory.getInstance().createIRI(value.stringValue());
9697
}
9798

9899
static Value getPossibleSingleton(RepositoryConnection repositoryConnection, Resource id,
99-
URI predicate) throws RepositoryException, BridgeDBException {
100+
IRI predicate) throws RepositoryException, BridgeDBException {
100101
RepositoryResult<Statement> statements =
101102
repositoryConnection.getStatements(id, predicate, null, true);
102103
if (statements.hasNext()) {
@@ -111,7 +112,7 @@ static Value getPossibleSingleton(RepositoryConnection repositoryConnection, Res
111112
return null;
112113
}
113114

114-
static Set<String> getAllStrings(RepositoryConnection repositoryConnection, Resource id, URI predicate)
115+
static Set<String> getAllStrings(RepositoryConnection repositoryConnection, Resource id, IRI predicate)
115116
throws RepositoryException {
116117
HashSet<String> results = new HashSet<String>();
117118
RepositoryResult<Statement> statements =
@@ -123,7 +124,7 @@ static Set<String> getAllStrings(RepositoryConnection repositoryConnection, Reso
123124
return results;
124125
}
125126

126-
static Set<Resource> getAllResources(RepositoryConnection repositoryConnection, Resource id, URI predicate)
127+
static Set<Resource> getAllResources(RepositoryConnection repositoryConnection, Resource id, IRI predicate)
127128
throws RepositoryException {
128129
HashSet<Resource> results = new HashSet<Resource>();
129130
RepositoryResult<Statement> statements =

‎org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java‎

Lines changed: 9 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -27,18 +27,17 @@
2727
import java.util.SortedSet;
2828
import java.util.TreeSet;
2929
import java.util.regex.Pattern;
30+
3031
import org.bridgedb.DataSource;
3132
import org.bridgedb.DataSourcePatterns;
3233
import org.bridgedb.bio.DataSourceTxt;
3334
import org.bridgedb.rdf.constants.BridgeDBConstants;
34-
import org.bridgedb.rdf.constants.IdenitifiersOrgConstants;
3535
import org.bridgedb.rdf.constants.RdfConstants;
3636
import org.bridgedb.rdf.identifiers.org.IdentifersOrgReader;
3737
import org.bridgedb.utils.BridgeDBException;
38+
import org.eclipse.rdf4j.model.IRI;
3839
import org.eclipse.rdf4j.model.Resource;
39-
import org.eclipse.rdf4j.model.URI;
40-
import org.eclipse.rdf4j.model.impl.LiteralImpl;
41-
import org.eclipse.rdf4j.model.impl.URIImpl;
40+
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
4241
import org.eclipse.rdf4j.repository.RepositoryConnection;
4342
import org.eclipse.rdf4j.repository.RepositoryException;
4443

@@ -59,7 +58,7 @@ public class UriPattern extends RdfBase implements Comparable<UriPattern>{
5958
private static HashMap<String,Set<UriPattern>> byCode = new HashMap<String,Set<UriPattern>>();
6059
static boolean initialized = false;
6160

62-
private static HashSet<URI> expectedPredicates = new HashSet<URI>(Arrays.asList(new URI[] {
61+
private static HashSet<IRI> expectedPredicates = new HashSet<IRI>(Arrays.asList(new IRI[] {
6362
BridgeDBConstants.HAS_POSTFIX_URI,
6463
BridgeDBConstants.HAS_PREFIX_URI,
6564
RdfConstants.TYPE_URI,
@@ -201,8 +200,8 @@ public static UriPattern existingByPrefixAndPostfix(String prefix, String postfi
201200
return existingByPattern(prefix + "$id" + postfix);
202201
}
203202

204-
public final URI getResourceId(){
205-
return new URIImpl(getUriPattern());
203+
public final IRI getResourceId(){
204+
return SimpleValueFactory.getInstance().createIRI(getUriPattern());
206205
}
207206

208207
public String getUriPattern() {
@@ -221,11 +220,11 @@ public static void addAll(RepositoryConnection repositoryConnection)
221220
}
222221

223222
public void add(RepositoryConnection repositoryConnection) throws RepositoryException{
224-
URI id = getResourceId();
223+
IRI id = getResourceId();
225224
repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.URI_PATTERN_URI);
226-
repositoryConnection.add(id, BridgeDBConstants.HAS_PREFIX_URI, new LiteralImpl(prefix));
225+
repositoryConnection.add(id, BridgeDBConstants.HAS_PREFIX_URI, SimpleValueFactory.getInstance().createLiteral(prefix));
227226
if (!postfix.isEmpty()){
228-
repositoryConnection.add(id, BridgeDBConstants.HAS_POSTFIX_URI, new LiteralImpl(postfix));
227+
repositoryConnection.add(id, BridgeDBConstants.HAS_POSTFIX_URI, SimpleValueFactory.getInstance().createLiteral(postfix));
229228
}
230229
}
231230

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