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Development for release 3.1.1 #233

Merged
merged 8 commits into from
Dec 18, 2023
Merged

Development for release 3.1.1 #233

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b031932
Open for development
egonw Dec 2, 2023
4ac23f9
slf4j 2.0.9
egonw Dec 2, 2023
665f89f
Updated RDF4J to 4.0.0
egonw Dec 2, 2023
32b6d33
Updated RDF4J to 4.3.8
egonw Dec 2, 2023
6cd348e
BridgeDb Datasources 20231202
egonw Dec 2, 2023
2ab0822
Updated to match the new BridgeDb Datasources
egonw Dec 2, 2023
13a62d7
Two further updates for JUnit
egonw Dec 2, 2023
58f42e0
Log4j 2.22
egonw Dec 18, 2023
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2 changes: 1 addition & 1 deletion examples/pom.xml
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Expand Up @@ -3,7 +3,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.0</version>
<version>3.1.1-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<groupId>org.bridgedb.examples</groupId>
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2 changes: 1 addition & 1 deletion org.bridgedb.bio/pom.xml
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Expand Up @@ -8,7 +8,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.0</version>
<version>3.1.1-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv
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Expand Up @@ -54,7 +54,7 @@ ICD-11 ICD11 http://www.who.int/classifications/icd/en/ 1A95 unknown Homo sapie
Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 Il ILMN_\d+ Illumina illumina.probe probe
InChIKey Ik http://inchi.org/ QTBSBXVTEAMEQO-UHFFFAOYSA-N metabolite 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? Standard InChIKey P235 inchikey metabolite
IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id EBI-2307691 interaction 1 urn:miriam:intact ^EBI\-[0-9]+$ IntAct intact interaction
InterPro I http://www.ebi.ac.uk/interpro/ http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein
InterPro I http://www.ebi.ac.uk/interpro/ https://www.ebi.ac.uk/interpro/entry/InterPro/$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein
IPI Ip http://www.ebi.ac.uk/IPI http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$id&format=default IPI00000001 protein 1 ^IPI\d{8}$ IPI interpro protein
IRGSP Gene Ir http://rgp.dna.affrc.go.jp/IRGSP/ https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$id Os12g0561000 gene 1 Ir Os\d{2}g\d+ IRGSP Gene rapdb.locus gene
ISBN isbn http://isbndb.com/ http://isbndb.com/search-all.html?kw=$id 9781584885658 publication 1 urn:miriam:isbn ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ ISBN P212 isbn publication
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2 changes: 1 addition & 1 deletion org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv
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Expand Up @@ -54,7 +54,7 @@ ICD-11 ICD11 http://www.who.int/classifications/icd/en/ 1A95 unknown Homo sapie
Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 Il ILMN_\d+ Illumina illumina.probe probe
InChIKey Ik http://inchi.org/ QTBSBXVTEAMEQO-UHFFFAOYSA-N metabolite 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? Standard InChIKey P235 inchikey metabolite
IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id EBI-2307691 interaction 1 urn:miriam:intact ^EBI\-[0-9]+$ IntAct intact interaction
InterPro I http://www.ebi.ac.uk/interpro/ http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein
InterPro I http://www.ebi.ac.uk/interpro/ https://www.ebi.ac.uk/interpro/entry/InterPro/$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein
IPI Ip http://www.ebi.ac.uk/IPI http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$id&format=default IPI00000001 protein 1 ^IPI\d{8}$ IPI interpro protein
IRGSP Gene Ir http://rgp.dna.affrc.go.jp/IRGSP/ https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$id Os12g0561000 gene 1 Ir Os\d{2}g\d+ IRGSP Gene rapdb.locus gene
ISBN isbn http://isbndb.com/ http://isbndb.com/search-all.html?kw=$id 9781584885658 publication 1 urn:miriam:isbn ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ ISBN P212 isbn publication
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2 changes: 1 addition & 1 deletion org.bridgedb.file.orthoxml/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.0</version>
<version>3.1.1-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.gui/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.0</version>
<version>3.1.1-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.rdb.construct/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.0</version>
<version>3.1.1-SNAPSHOT</version>
</parent>

<build>
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4 changes: 2 additions & 2 deletions org.bridgedb.rdb/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.0</version>
<version>3.1.1-SNAPSHOT</version>
</parent>

<build>
Expand Down Expand Up @@ -108,7 +108,7 @@
<dependency>
<groupId>org.junit.platform</groupId>
<artifactId>junit-platform-launcher</artifactId>
<version>1.9.3</version>
<version>1.10.1</version>
<scope>test</scope>
</dependency>
<dependency>
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2 changes: 1 addition & 1 deletion org.bridgedb.rdf/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.0</version>
<version>3.1.1-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.rdf/resources/DataSource.ttl
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Expand Up @@ -646,7 +646,7 @@ bridgeDB:DataSource_InterPro a bridgeDB:DataSource ;
bridgeDB:idExample "IPR000100" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "protein" ;
bridgeDB:hasPrimaryUriPattern <http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=$id> ;
bridgeDB:hasPrimaryUriPattern <https://www.ebi.ac.uk/interpro/entry/InterPro/$id> ;
bridgeDB:hasIdentifiersOrgPattern <http://identifiers.org/interpro/$id> ;
bridgeDB:hasUriPattern <http://bio2rdf.org/interpro:$id> .

Expand Down
8 changes: 4 additions & 4 deletions org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl
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@@ -1,4 +1,4 @@
@prefix bridgeDB: <http://vocabularies.bridgedb.org/ops#> .
@prefix bridgeDB: <http://vocabularies.bridgedb.org/ops#> .
@prefix dcat: <http://www.w3.org/ns/dcat#> .
@prefix dcterms: <http://purl.org/dc/terms/> .

Expand Down Expand Up @@ -3101,7 +3101,7 @@ bridgeDB:DataSource_InterPro a bridgeDB:DataSource ;
bridgeDB:idExample "IPR000100" ;
bridgeDB:primary "true"^^<http://www.w3.org/2001/XMLSchema#boolean> ;
bridgeDB:type "protein" ;
bridgeDB:hasPrimaryUriPattern <http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=$id> ;
bridgeDB:hasPrimaryUriPattern <https://www.ebi.ac.uk/interpro/entry/InterPro/$id> ;
bridgeDB:hasIdentifiersOrgPattern <http://identifiers.org/interpro/$id> ;
bridgeDB:hasIdentifiersOrgInfoPattern <http://info.identifiers.org/interpro/$id> ;
bridgeDB:hasRegexPattern "^IPR\\d{6}$" ;
Expand Down Expand Up @@ -11427,8 +11427,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ;
<http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id> a bridgeDB:UriPattern ;
bridgeDB:hasPrefix "http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=" .

<http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=$id> a bridgeDB:UriPattern ;
bridgeDB:hasPrefix "http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=" .
<https://www.ebi.ac.uk/interpro/entry/InterPro/$id> a bridgeDB:UriPattern ;
bridgeDB:hasPrefix "https://www.ebi.ac.uk/interpro/entry/InterPro/" .

<http://www.ebi.ac.uk/interpro/entry/$id> a bridgeDB:UriPattern ;
bridgeDB:hasPrefix "http://www.ebi.ac.uk/interpro/entry/" .
Expand Down
44 changes: 19 additions & 25 deletions org.bridgedb.rdf/src/org/bridgedb/rdf/BridgeDBRdfHandler.java
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Expand Up @@ -47,9 +47,7 @@
import org.eclipse.rdf4j.model.Resource;
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.model.Value;
import org.eclipse.rdf4j.model.impl.BooleanLiteralImpl;
import org.eclipse.rdf4j.model.impl.LiteralImpl;
import org.eclipse.rdf4j.model.impl.URIImpl;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.repository.Repository;
import org.eclipse.rdf4j.repository.RepositoryConnection;
import org.eclipse.rdf4j.repository.RepositoryException;
Expand Down Expand Up @@ -86,7 +84,7 @@
RepositoryConnection repositoryConnection = null;
try {
repository = new SailRepository(new MemoryStore());
repository.initialize();
repository.init();
repositoryConnection = repository.getConnection();
repositoryConnection.add(stream, DEFAULT_BASE_URI, DEFAULT_FILE_FORMAT);
readAllDataSources(repositoryConnection);
Expand Down Expand Up @@ -216,7 +214,7 @@

private void readCodeMapper(RepositoryConnection repositoryConnection, String systemCode, Pattern regex) throws RepositoryException, BridgeDBException {
RepositoryResult<Statement> statements =
repositoryConnection.getStatements(null, BridgeDBConstants.SYSTEM_CODE_URI, new LiteralImpl(systemCode), true);
repositoryConnection.getStatements(null, BridgeDBConstants.SYSTEM_CODE_URI, SimpleValueFactory.getInstance().createLiteral(systemCode), true);
// String xrefPrefix = null;
Resource codeMapperReseource = null;
while (statements.hasNext()) {
Expand Down Expand Up @@ -321,7 +319,7 @@
RepositoryConnection repositoryConnection = null;
try {
repository = new SailRepository(new MemoryStore());
repository.initialize();
repository.init();

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repositoryConnection = repository.getConnection();
for (DataSource dataSource: dataSources){
writeDataSource(repositoryConnection, dataSource);
Expand All @@ -341,29 +339,25 @@
repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.DATA_SOURCE_URI);

if (dataSource.getFullName() != null){
repositoryConnection.add(id, BridgeDBConstants.FULL_NAME_URI, new LiteralImpl(dataSource.getFullName()));
repositoryConnection.add(id, BridgeDBConstants.FULL_NAME_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getFullName()));

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}

if (dataSource.getSystemCode() != null && (!dataSource.getSystemCode().trim().isEmpty())){
repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, new LiteralImpl(dataSource.getSystemCode()));
repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getSystemCode()));

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}

if (dataSource.getMainUrl() != null){
repositoryConnection.add(id, BridgeDBConstants.MAIN_URL_URI, new LiteralImpl(dataSource.getMainUrl()));
repositoryConnection.add(id, BridgeDBConstants.MAIN_URL_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getMainUrl()));

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}

if (dataSource.getExample() != null && dataSource.getExample().getId() != null){
repositoryConnection.add(id, BridgeDBConstants.ID_EXAMPLE_URI, new LiteralImpl(dataSource.getExample().getId()));
repositoryConnection.add(id, BridgeDBConstants.ID_EXAMPLE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getExample().getId()));

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}

if (dataSource.isPrimary()){
repositoryConnection.add(id, BridgeDBConstants.PRIMARY_URI, BooleanLiteralImpl.TRUE);
} else {
repositoryConnection.add(id, BridgeDBConstants.PRIMARY_URI, BooleanLiteralImpl.FALSE);
}
repositoryConnection.add(id, BridgeDBConstants.PRIMARY_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.isPrimary()));

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if (dataSource.getType() != null){
repositoryConnection.add(id, BridgeDBConstants.TYPE_URI, new LiteralImpl(dataSource.getType()));
repositoryConnection.add(id, BridgeDBConstants.TYPE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getType()));

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}

Pattern regex = DataSourcePatterns.getPatterns().get(dataSource);
Expand Down Expand Up @@ -391,16 +385,16 @@

Pattern pattern = DataSourcePatterns.getPatterns().get(dataSource);
if (pattern != null && !pattern.toString().isEmpty()){
Value patternValue = new LiteralImpl(pattern.toString());
Value patternValue = SimpleValueFactory.getInstance().createLiteral(pattern.toString());

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repositoryConnection.add(id, BridgeDBConstants.HAS_REGEX_PATTERN_URI, patternValue);
}

if (dataSource.getAlternative() != null){
repositoryConnection.add(id, DCTermsConstants.ALTERNATIVE_URI, new LiteralImpl(dataSource.getAlternative()));
repositoryConnection.add(id, DCTermsConstants.ALTERNATIVE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getAlternative()));

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}

if (dataSource.getDescription() != null){
repositoryConnection.add(id, DCatConstants.DESCRIPTION_URI, new LiteralImpl(dataSource.getDescription()));
repositoryConnection.add(id, DCatConstants.DESCRIPTION_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getDescription()));

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}

SortedSet<UriPattern> sortedPatterns = UriPattern.byCodeAndType(dataSource.getSystemCode(), UriPatternType.dataSourceUriPattern);
Expand All @@ -421,8 +415,8 @@
}
Resource id = asCodeMapperResource(dataSource);
repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.CODE_MAPPER_URI);
repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, new LiteralImpl(dataSource.getSystemCode()));
Value prefixValue = new LiteralImpl(xrefPrefix);
repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getSystemCode()));
Value prefixValue = SimpleValueFactory.getInstance().createLiteral(xrefPrefix);

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repositoryConnection.add(id, BridgeDBConstants.XREF_PREFIX_URI, prefixValue);

SortedSet<UriPattern> sortedPatterns = UriPattern.byCodeAndType(dataSource.getSystemCode(), UriPatternType.codeMapperPattern);
Expand Down Expand Up @@ -476,17 +470,17 @@

protected static Resource asResource(DataSource dataSource) {
if (dataSource.getFullName() == null){
return new URIImpl(BridgeDBConstants.DATA_SOURCE1 + "_bysysCode_" + scrub(dataSource.getSystemCode()));
return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.DATA_SOURCE1 + "_bysysCode_" + scrub(dataSource.getSystemCode()));

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} else {
return new URIImpl(BridgeDBConstants.DATA_SOURCE1 + "_" + scrub(dataSource.getFullName()));
return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.DATA_SOURCE1 + "_" + scrub(dataSource.getFullName()));
}
}

protected static Resource asCodeMapperResource(DataSource dataSource) {
if (dataSource.getFullName() == null){
return new URIImpl(BridgeDBConstants.CODE_MAPPER1 + "_bysysCode_" + scrub(dataSource.getSystemCode()));
return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.CODE_MAPPER1 + "_bysysCode_" + scrub(dataSource.getSystemCode()));

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} else {
return new URIImpl(BridgeDBConstants.CODE_MAPPER1 + "_" + scrub(dataSource.getFullName()));
return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.CODE_MAPPER1 + "_" + scrub(dataSource.getFullName()));

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}
}

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18 changes: 9 additions & 9 deletions org.bridgedb.rdf/src/org/bridgedb/rdf/OrganismRdf.java
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Expand Up @@ -22,16 +22,16 @@
import java.io.IOException;
import java.util.HashMap;
import java.util.Set;

import org.bridgedb.bio.Organism;
import org.bridgedb.rdf.constants.BridgeDBConstants;
import org.bridgedb.rdf.constants.RdfConstants;
import org.bridgedb.utils.BridgeDBException;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Resource;
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.model.URI;
import org.eclipse.rdf4j.model.Value;
import org.eclipse.rdf4j.model.impl.LiteralImpl;
import org.eclipse.rdf4j.model.impl.URIImpl;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.repository.RepositoryConnection;
import org.eclipse.rdf4j.repository.RepositoryException;
import org.eclipse.rdf4j.rio.RDFHandler;
Expand Down Expand Up @@ -64,8 +64,8 @@
return scrub(organism.code());
}

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

public static void addAll(RepositoryConnection repositoryConnection) throws IOException, RepositoryException {
Expand All @@ -82,11 +82,11 @@

public static void add(RepositoryConnection repositoryConnection, Organism organism)
throws IOException, RepositoryException {
URI id = getResourceId(organism);
IRI id = getResourceId(organism);

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repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.ORGANISM_URI);
repositoryConnection.add(id, BridgeDBConstants.CODE_URI, new LiteralImpl(organism.code()));
repositoryConnection.add(id, BridgeDBConstants.SHORT_NAME_URI, new LiteralImpl(organism.shortName()));
repositoryConnection.add(id, BridgeDBConstants.LATIN_NAME_URI, new LiteralImpl(organism.latinName()));
repositoryConnection.add(id, BridgeDBConstants.CODE_URI, SimpleValueFactory.getInstance().createLiteral(organism.code()));
repositoryConnection.add(id, BridgeDBConstants.SHORT_NAME_URI, SimpleValueFactory.getInstance().createLiteral(organism.shortName()));
repositoryConnection.add(id, BridgeDBConstants.LATIN_NAME_URI, SimpleValueFactory.getInstance().createLiteral(organism.latinName()));

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org.bridgedb.rdf/src/org/bridgedb/rdf/OrganismRdf.java#L87-L89 

Added lines #L87 - L89 were not covered by tests
}

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