excludedFromStemming ) {
+ return getSubjectIndex( name, DEFAULT_INDEXABLE_PROPERTIES, excludedFromStemming );
+ }
+
+ /**
+ * Obtain an index with default analyzer (English), or null if no index is available.
+ *
+ * DOES not create the index if it doesn't exist.
+ */
+ @Nullable
+ public static SearchIndex getSubjectIndex( String name, Collection indexableProperties, Set excludedFromStemming ) {
+ log.debug( "Loading index for {}...", name );
try {
// we do not put this in the try-with-open because we want these to *stay* open
- FSDirectory directory = FSDirectory.open( indexdir );
- FSDirectory directorystd = FSDirectory.open( indexdirstd );
-
+ FSDirectory directory = FSDirectory.open( getIndexPath( name ).toFile() );
+ FSDirectory directoryStd = FSDirectory.open( getIndexPath( name + ".std" ).toFile() );
if ( !IndexReader.indexExists( directory ) ) {
return null;
}
- if ( !IndexReader.indexExists( directorystd ) ) {
+ if ( !IndexReader.indexExists( directoryStd ) ) {
return null;
}
-
- IndexReader reader = IndexReader.open( directory );
- IndexReader readerstd = IndexReader.open( directorystd );
- MultiReader r = new MultiReader( reader, readerstd );
- return new SearchIndex( r, analyzer );
-
+ return openIndex( directory, directoryStd, indexableProperties, excludedFromStemming );
} catch ( IOException e ) {
- log.warn( "Index for " + name + " could not be read: " + e.getMessage() );
+ log.warn( "Index for {} could not be opened.", name, e );
return null;
}
}
/**
- * Create an on-disk index from an existing OntModel. Any existing index will be deleted/overwritten.
+ * Index an ontology with the default indexable properties.
*/
- private static SearchIndex index( String name, OntModel model ) throws JenaException, IOException {
+ public static SearchIndex indexOntology( String name, OntModel model, Set excludedFromStemming, boolean force ) throws JenaException, IOException {
+ return indexOntology( name, model, DEFAULT_INDEXABLE_PROPERTIES, excludedFromStemming, force );
+ }
- File indexdir = getIndexPath( name );
+ /**
+ * Loads or creates an index from an existing OntModel. Any existing index will loaded unless force=true. It will be
+ * created if there isn't one already, or if force=true.
+ */
+ public static SearchIndex indexOntology( String name, OntModel model, Collection indexableProperties, Set excludedFromStemming, boolean force ) throws JenaException, IOException {
+ if ( force ) {
+ return index( name, model, indexableProperties, excludedFromStemming );
+ }
+ SearchIndex index = getSubjectIndex( name, excludedFromStemming );
+ if ( index == null ) {
+ log.warn( "Index not found, or there was an error, re-indexing {}...", name );
+ return index( name, model, indexableProperties, excludedFromStemming );
+ }
+ log.debug( "A valid index for {} already exists, using", name );
+ return index;
+ }
- StopWatch timer = new StopWatch();
- timer.start();
- FSDirectory dir = FSDirectory.open( indexdir );
- log.info( "Indexing " + name + " to: " + indexdir );
+ private static Path getIndexPath( String name ) {
+ if ( StringUtils.isBlank( name ) ) {
+ throw new IllegalArgumentException( "The ontology must have a suitable name for being indexed." );
+ }
+ String ontologyDir = Configuration.getString( "ontology.index.dir" ); // e.g., /something/gemmaData/compass
+ if ( StringUtils.isBlank( ontologyDir ) ) {
+ return Paths.get( System.getProperty( "java.io.tmpdir" ), "searchIndices", "ontology", name );
+ }
+ return Paths.get( ontologyDir, "ontology", name );
+ }
- /*
- * adjust the analyzer ...
- */
- Analyzer analyzer = new EnglishAnalyzer( Version.LUCENE_36 );
+ /**
+ * Create an on-disk index from an existing OntModel. Any existing index will be deleted/overwritten.
+ */
+ private static SearchIndex index( String name, OntModel model, Collection indexableProperties, Set excludedFromStemming ) throws JenaException, IOException {
+ Directory dir = index( name, model, new EnglishAnalyzer( Version.LUCENE_36, EnglishAnalyzer.getDefaultStopSet(), excludedFromStemming ), getIndexPath( name ), indexableProperties );
+ // we need to also analyze using the Standard analyzer, which doesn't do stemming and allows wildcard.
+ Directory dirStd = index( name, model, new StandardAnalyzer( Version.LUCENE_36 ), getIndexPath( name + ".std" ), indexableProperties );
+ return openIndex( dir, dirStd, indexableProperties, excludedFromStemming );
+ }
+
+ private static Directory index( String name, OntModel model, Analyzer analyzer, Path indexDir, Collection indexableProperties ) throws IOException {
+ StopWatch timer = StopWatch.createStarted();
+ FSDirectory dir = FSDirectory.open( indexDir.toFile() );
+ log.debug( "Indexing {} to: {}...", name, indexDir );
IndexWriterConfig config = new IndexWriterConfig( Version.LUCENE_36, analyzer );
- IndexWriter indexWriter = new IndexWriter( dir, config );
- indexWriter.deleteAll(); // start with clean slate.
- assert 0 == indexWriter.numDocs();
+ try ( IndexWriter indexWriter = new IndexWriter( dir, config ) ) {
+ indexWriter.deleteAll(); // start with clean slate.
+ assert 0 == indexWriter.numDocs();
+ Map indexablePropertiesByField = indexableProperties.stream()
+ .collect( Collectors.toMap( p -> p.getProperty().getURI(), p -> p ) );
+ ExtendedIterator subjects = model.listSubjects()
+ .filterDrop( new BnodeFilter<>() );
+ while ( subjects.hasNext() ) {
+ Resource subject = subjects.next();
+ String id = subject.getURI();
+ Document doc = new Document();
+ doc.add( new Field( ID_FIELD, id, Field.Store.YES, Field.Index.NOT_ANALYZED ) );
+ doc.add( new Field( LOCAL_NAME_FIELD, subject.getLocalName(), Field.Store.NO, Field.Index.NOT_ANALYZED ) );
+ boolean isClass, isIndividual;
+ if ( subject.canAs( OntResource.class ) ) {
+ isClass = subject.as( OntResource.class ).isClass();
+ isIndividual = subject.as( OntResource.class ).isIndividual();
+ } else {
+ isClass = false;
+ isIndividual = false;
+ }
+ doc.add( new NumericField( IS_CLASS_FIELD ).setIntValue( isClass ? 1 : 0 ) );
+ doc.add( new NumericField( IS_INDIVIDUAL_FIELD ).setIntValue( isIndividual ? 1 : 0 ) );
+ for ( IndexableProperty prop : indexableProperties ) {
+ StmtIterator listStatements = subject.listProperties( prop.property );
+ while ( listStatements.hasNext() ) {
+ Statement s = listStatements.next();
+ String field = s.getPredicate().getURI();
+ Fieldable f;
+ if ( s.getObject().isLiteral() ) {
+ Literal l = s.getObject().asLiteral();
+ Object v;
+ try {
+ v = l.getValue();
+ } catch ( DatatypeFormatException e ) {
+ log.warn( "Invalid datatype for literal: {}", l, e );
+ continue;
+ }
+ if ( v instanceof String ) {
+ f = new Field( field, ( String ) v, Field.Store.NO, indexablePropertiesByField.get( field ).isAnalyzed() ? Field.Index.ANALYZED : Field.Index.NOT_ANALYZED );
+ } else if ( v instanceof Number ) {
+ NumericField nf = new NumericField( field );
+ if ( v instanceof Integer ) {
+ nf.setIntValue( ( Integer ) v );
+ } else if ( v instanceof Long ) {
+ nf.setLongValue( ( Long ) v );
+ } else if ( v instanceof Float ) {
+ nf.setFloatValue( ( Float ) v );
+ } else if ( v instanceof Double ) {
+ nf.setDoubleValue( ( Double ) v );
+ } else {
+ log.warn( "Skipping numeric literal of unsupported type: {}", l );
+ continue;
+ }
+ f = nf;
+ } else if ( v instanceof XSDDateTime ) {
+ f = new NumericField( field )
+ .setLongValue( ( ( XSDDateTime ) v ).asCalendar().getTime().getTime() );
+ } else if ( v instanceof Boolean ) {
+ f = new NumericField( field ).setIntValue( Boolean.TRUE.equals( v ) ? 1 : 0 );
+ } else {
+ log.warn( "Skipping literal of unsupported type: {}", l );
+ continue;
+ }
+ } else if ( s.getObject().isURIResource() ) {
+ // index the URI
+ f = new Field( field, s.getObject().asResource().getURI(), Field.Store.NO, Field.Index.NOT_ANALYZED );
+ } else {
+ // could be a blank node
+ continue;
+ }
+ if ( isIndividual ) {
+ System.out.println( doc );
+ }
+ doc.add( f );
+ }
+ }
+ indexWriter.addDocument( doc );
+ }
+ indexWriter.commit();
+ log.debug( "Done indexing {} subjects of {} in {} s.", indexWriter.numDocs(), name, String.format( "%.2f", timer.getTime() / 1000.0 ) );
+ }
+ return dir;
+ }
- IndexBuilderSubject larqSubjectBuilder = new IndexBuilderSubject( indexWriter );
- StmtIterator listStatements = model.listStatements( new IndexerSelector() );
- larqSubjectBuilder.indexStatements( listStatements );
- indexWriter.commit();
- log.info( indexWriter.numDocs() + " Statements indexed..." );
- indexWriter.close();
+ private static SearchIndex openIndex( Directory dir, Directory dirStd, Collection indexableProperties, Set excludedFromStemming ) throws IOException {
+ String[] searchableFields = Stream.concat( Stream.of( ID_FIELD, LOCAL_NAME_FIELD ), indexableProperties.stream().map( p -> p.property ).map( Resource::getURI ) )
+ .distinct()
+ .toArray( String[]::new );
+ return new LuceneSearchIndex( searchableFields, new MultiReader( IndexReader.open( dir ), IndexReader.open( dirStd ) ), new EnglishAnalyzer( Version.LUCENE_36, EnglishAnalyzer.getDefaultStopSet(), excludedFromStemming ) );
+ }
- Directory dirstd = indexStd( name, model );
+ private static class LuceneSearchIndex implements SearchIndex {
- MultiReader r = new MultiReader( IndexReader.open( dir ), IndexReader.open( dirstd ) );
+ private static final Logger log = LoggerFactory.getLogger( LuceneSearchIndex.class );
- // workaround to get the EnglishAnalyzer.
- SearchIndex index = new SearchIndex( r, new EnglishAnalyzer( Version.LUCENE_36 ) );
- // larqSubjectBuilder.getIndex(); // always returns a StandardAnalyazer
- assert index.getLuceneQueryParser().getAnalyzer() instanceof EnglishAnalyzer;
+ private final String[] searchableFields;
+ private final IndexReader index;
+ private final Analyzer analyzer;
- log.info( "Done indexing of " + name + " in " + String.format( "%.2f", timer.getTime() / 1000.0 ) + "s" );
+ public LuceneSearchIndex( String[] searchableFields, IndexReader index, Analyzer analyzer ) {
+ this.searchableFields = searchableFields;
+ this.index = index;
+ this.analyzer = analyzer;
+ }
- return index;
- }
+ @Override
+ public ExtendedIterator search( OntModel model, String queryString, int maxResults ) throws OntologySearchException {
+ return search( model, queryString, null, maxResults );
+ }
- /**
- * We need to also analyze using the Standard analyzer, which doesn't do stemming and allows wildcard.
- */
- private static Directory indexStd( String name, OntModel model ) throws JenaException, IOException {
+ @Override
+ public ExtendedIterator searchClasses( OntModel model, String queryString, int maxResults ) throws OntologySearchException {
+ return search( model, queryString, NumericRangeFilter.newIntRange( IS_CLASS_FIELD, 1, 1, true, true ), maxResults );
+ }
- File file = getIndexPath( name + ".std" );
+ @Override
+ public ExtendedIterator searchIndividuals( OntModel model, String queryString, int maxResults ) throws OntologySearchException {
+ return search( model, queryString, NumericRangeFilter.newIntRange( IS_INDIVIDUAL_FIELD, 1, 1, true, true ), maxResults );
+ }
- FSDirectory dir = FSDirectory.open( file );
- dir.getLockFactory().clearLock( dir.getLockID() );
- log.info( "Index to: " + file );
- Analyzer analyzer = new StandardAnalyzer( Version.LUCENE_36 );
- IndexWriterConfig config = new IndexWriterConfig( Version.LUCENE_36, analyzer );
- IndexWriter indexWriter = new IndexWriter( dir, config );
- indexWriter.deleteAll();
- IndexBuilderSubject larqSubjectBuilder = new IndexBuilderSubject( indexWriter );
- StmtIterator listStatements = model.listStatements( new IndexerSelector() );
- larqSubjectBuilder.indexStatements( listStatements );
- indexWriter.commit();
- log.info( indexWriter.numDocs() + " Statements indexed..." );
- indexWriter.close();
- return dir;
+ private ExtendedIterator search( OntModel model, String queryString, @Nullable Filter filter, int maxResults ) throws OntologySearchException {
+ if ( StringUtils.isBlank( queryString ) ) {
+ throw new IllegalArgumentException( "Query cannot be blank" );
+ }
+ StopWatch timer = StopWatch.createStarted();
+ try {
+ Query query = new MultiFieldQueryParser( Version.LUCENE_36, searchableFields, analyzer ).parse( queryString );
+ // in general, results are found in both regular and std index, so we divide by 2 the initial capacity
+ // we also have to double the number of hits to account for duplicates
+ TopDocs hits = new IndexSearcher( index ).search( query, filter, maxResults * 2 );
+ Set seenIds = new HashSet<>( hits.totalHits / 2 );
+ List resources = new ArrayList<>( hits.totalHits / 2 );
+ for ( int i = 0; i < hits.scoreDocs.length; i++ ) {
+ Document doc = index.document( hits.scoreDocs[i].doc );
+ String id = doc.get( ID_FIELD );
+ if ( seenIds.contains( id ) ) {
+ continue;
+ }
+ Resource res = model.getResource( id );
+ resources.add( new JenaSearchResult( res, hits.scoreDocs[i].score ) );
+ seenIds.add( id );
+ if ( seenIds.size() >= maxResults ) {
+ break;
+ }
+ }
+ return WrappedIterator.create( resources.iterator() );
+ } catch ( ParseException e ) {
+ throw new OntologySearchException( "Failed to parse search query.", queryString, e );
+ } catch ( IOException e ) {
+ throw new OntologySearchException( "An I/O error occured while searching.", queryString, e );
+ } finally {
+ timer.stop();
+ if ( timer.getTime() > 100 ) {
+ log.warn( "Ontology resource search for: {} took {} ms.", queryString, timer.getTime() );
+ }
+ }
+ }
+
+ @Override
+ public void close() throws IOException {
+ index.close();
+ }
}
+
}
diff --git a/src/ubic/basecode/ontology/jena/OntologyIndividualImpl.java b/src/ubic/basecode/ontology/jena/OntologyIndividualImpl.java
index 61731377..e888875f 100644
--- a/src/ubic/basecode/ontology/jena/OntologyIndividualImpl.java
+++ b/src/ubic/basecode/ontology/jena/OntologyIndividualImpl.java
@@ -44,12 +44,6 @@ public OntologyIndividualImpl( Individual ind, Set additionalRestri
this.additionalRestrictions = additionalRestrictions;
}
- public OntologyIndividualImpl( Individual ind, Set additionalRestrictions, double score ) {
- super( ind, score );
- this.ind = ind;
- this.additionalRestrictions = additionalRestrictions;
- }
-
@Override
public OntologyTerm getInstanceOf() {
Resource type = ind.getRDFType();
diff --git a/src/ubic/basecode/ontology/jena/OntologyLoader.java b/src/ubic/basecode/ontology/jena/OntologyLoader.java
index 38c27a7c..f31278b4 100644
--- a/src/ubic/basecode/ontology/jena/OntologyLoader.java
+++ b/src/ubic/basecode/ontology/jena/OntologyLoader.java
@@ -52,18 +52,18 @@ class OntologyLoader {
private static final String OLD_CACHE_SUFFIX = ".old";
private static final String TMP_CACHE_SUFFIX = ".tmp";
- public static OntModel loadMemoryModel( InputStream is, String url ) throws JenaException {
+ public static OntModel loadMemoryModel( InputStream is, String url ) throws JenaException, IOException {
return loadMemoryModel( is, url, true );
}
/**
* Load an ontology into memory. Use this type of model when fast access is critical and memory is available.
*/
- public static OntModel loadMemoryModel( InputStream is, String url, boolean processImports ) throws JenaException {
+ public static OntModel loadMemoryModel( InputStream is, String url, boolean processImports ) throws JenaException, IOException {
return loadMemoryModel( is, url, processImports, OntModelSpec.OWL_MEM_TRANS_INF );
}
- public static OntModel loadMemoryModel( InputStream is, String url, boolean processImports, OntModelSpec spec ) throws JenaException {
+ public static OntModel loadMemoryModel( InputStream is, String url, boolean processImports, OntModelSpec spec ) throws JenaException, IOException {
OntModel model = getMemoryModel( url, processImports, spec );
model.read( is, null );
return model;
@@ -107,7 +107,7 @@ public static OntModel loadMemoryModel( String url, @Nullable String cacheName,
} catch ( ClosedByInterruptException e ) {
throw e;
} catch ( IOException e ) {
- log.error( "Failed to load ontology model for " + url + ", will attempt to load from disk.", e );
+ log.error( "Failed to load ontology model for {}, will attempt to load from disk.", url, e );
attemptToLoadFromDisk = true;
} finally {
if ( urlc instanceof HttpURLConnection ) {
@@ -129,7 +129,7 @@ public static OntModel loadMemoryModel( String url, @Nullable String cacheName,
// the ontology.
FileUtils.createParentDirectories( oldFile );
Files.copy( f.toPath(), oldFile.toPath(), StandardCopyOption.REPLACE_EXISTING );
- log.info( "Load model from disk: " + timer.getTime() + "ms" );
+ log.debug( "Load model from disk took {} ms", timer.getTime() );
}
} else {
throw new RuntimeException(
@@ -138,7 +138,7 @@ public static OntModel loadMemoryModel( String url, @Nullable String cacheName,
} else if ( tempFile.exists() ) {
// Model was successfully loaded into memory from URL with given cacheName
// Save cache to disk (rename temp file)
- log.info( "Caching ontology to disk: " + cacheName + " under " + f.getAbsolutePath() );
+ log.debug( "Caching ontology to disk: {} under {}", cacheName, f.getAbsolutePath() );
try {
// Need to compare previous to current so instead of overwriting we'll move the old file
if ( f.exists() ) {
@@ -149,12 +149,12 @@ public static OntModel loadMemoryModel( String url, @Nullable String cacheName,
}
Files.move( tempFile.toPath(), f.toPath(), StandardCopyOption.REPLACE_EXISTING );
} catch ( IOException e ) {
- log.error( "Failed to cache ontology " + url + " to disk.", e );
+ log.error( "Failed to cache ontology {} to disk.", url, e );
}
}
}
- log.info( "Loading ontology model for " + url + " took " + timer.getTime() + "ms" );
+ log.debug( "Loading ontology model for {} took {} ms", url, timer.getTime() );
return model;
}
@@ -236,7 +236,7 @@ public static URLConnection openConnection( String url ) throws IOException {
if ( StringUtils.isBlank( newUrl ) ) {
throw new RuntimeException( String.format( "Redirect response for %s is lacking a 'Location' header.", url ) );
}
- log.debug( "Redirect to " + newUrl + " from " + url );
+ log.debug( "Redirect to {} from {}", newUrl, url );
urlc = openConnectionInternal( newUrl );
}
}
@@ -251,7 +251,7 @@ private static URLConnection openConnectionInternal( String url ) throws IOExcep
if ( urlc instanceof HttpURLConnection ) {
( ( HttpURLConnection ) urlc ).setInstanceFollowRedirects( true );
}
- log.debug( "Connecting to " + url );
+ log.debug( "Connecting to {}", url );
urlc.connect(); // Will error here on bad URL
return urlc;
}
diff --git a/src/ubic/basecode/ontology/jena/OntologySearch.java b/src/ubic/basecode/ontology/jena/OntologySearch.java
deleted file mode 100644
index a51b9974..00000000
--- a/src/ubic/basecode/ontology/jena/OntologySearch.java
+++ /dev/null
@@ -1,148 +0,0 @@
-/*
- * The basecode project
- *
- * Copyright (c) 2007-2019 University of British Columbia
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-package ubic.basecode.ontology.jena;
-
-import com.hp.hpl.jena.ontology.ConversionException;
-import com.hp.hpl.jena.ontology.Individual;
-import com.hp.hpl.jena.ontology.OntClass;
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.shared.JenaException;
-import com.hp.hpl.jena.util.iterator.ExtendedIterator;
-import com.hp.hpl.jena.util.iterator.Map1Iterator;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang3.time.StopWatch;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import ubic.basecode.ontology.search.OntologySearchException;
-
-import java.util.Objects;
-import java.util.Optional;
-
-import static com.hp.hpl.jena.sparql.util.ModelUtils.convertGraphNodeToRDFNode;
-import static ubic.basecode.ontology.jena.JenaUtils.where;
-
-/**
- * @author pavlidis
- */
-class OntologySearch {
-
- private static final Logger log = LoggerFactory.getLogger( OntologySearch.class );
-
- /**
- * Find classes that match the query string.
- *
- * @param model that goes with the index
- * @param index to search
- * @return Collection of OntologyTerm objects
- */
- public static ExtendedIterator> matchClasses( OntModel model, SearchIndex index, String queryString ) throws OntologySearchException {
- return runSearch( model, index, queryString )
- .filterKeep( where( r -> r.result.isURIResource() && r.result.canAs( OntClass.class ) ) )
- .mapWith( r -> r.as( OntClass.class ) )
- .filterKeep( where( Objects::nonNull ) );
- }
-
- /**
- * Find individuals that match the query string
- *
- * @param model that goes with the index
- * @param index to search
- * @return Collection of OntologyTerm objects
- */
- public static ExtendedIterator> matchIndividuals( OntModel model, SearchIndex index, String queryString ) throws OntologySearchException {
- return runSearch( model, index, queryString )
- .filterKeep( where( r -> r.result.isURIResource() && r.result.canAs( Individual.class ) ) )
- .mapWith( r -> r.as( Individual.class ) )
- .filterKeep( where( Objects::nonNull ) );
- }
-
- /**
- * Find OntologyIndividuals and OntologyTerms that match the query string. Search with a wildcard is attempted
- * whenever possible.
- *
- * @param model that goes with the index
- * @param index to search
- * @return Collection of OntologyResource objects
- */
- public static ExtendedIterator> matchResources( OntModel model, SearchIndex index, String queryString ) throws OntologySearchException {
- return runSearch( model, index, queryString )
- .filterKeep( where( o -> o.result.isURIResource() && o.result.isResource() ) )
- .mapWith( r -> r.as( Resource.class ) )
- .filterKeep( where( Objects::nonNull ) );
- }
-
- private static ExtendedIterator> runSearch( Model model, SearchIndex index, String queryString ) throws OntologySearchJenaException {
- if ( StringUtils.isBlank( queryString ) ) {
- throw new IllegalArgumentException( "Query cannot be blank" );
- }
- StopWatch timer = StopWatch.createStarted();
- try {
- return new Map1Iterator<>( o -> new SearchResult<>( o.getLuceneDocId(), convertGraphNodeToRDFNode( o.getNode(), model ), o.getScore() ), index.search( queryString ) );
- } catch ( JenaException e ) {
- throw new OntologySearchJenaException( "Failed to search with query.", queryString, e );
- } finally {
- timer.stop();
- if ( timer.getTime() > 100 ) {
- log.warn( "Ontology resource search for: {} took {} ms.", queryString, timer.getTime() );
- }
- }
- }
-
- public static class SearchResult {
- public final int docId;
- public final T result;
- public final double score;
-
- private SearchResult( int docId, T result, double score ) {
- this.docId = docId;
- this.result = result;
- this.score = score;
- }
-
- @Override
- public boolean equals( Object obj ) {
- if ( obj instanceof SearchResult ) {
- return Objects.equals( result, ( ( SearchResult ) obj ).result );
- }
- return false;
- }
-
- @Override
- public int hashCode() {
- return Objects.hash( result );
- }
-
- @Override
- public String toString() {
- return String.format( "%s [docId = %d, score = %f]", result, docId, score );
- }
-
- private SearchResult as( Class clazz ) {
- try {
- return new SearchResult<>( docId, result.as( clazz ), score );
- } catch ( ConversionException e ) {
- log.warn( "Conversion of " + result + " to " + clazz.getName() + " failed.", e );
- return null;
- }
- }
- }
-}
diff --git a/src/ubic/basecode/ontology/jena/OntologySearchJenaException.java b/src/ubic/basecode/ontology/jena/OntologySearchJenaException.java
deleted file mode 100644
index bcb4cc71..00000000
--- a/src/ubic/basecode/ontology/jena/OntologySearchJenaException.java
+++ /dev/null
@@ -1,22 +0,0 @@
-package ubic.basecode.ontology.jena;
-
-import com.hp.hpl.jena.shared.JenaException;
-import ubic.basecode.ontology.search.OntologySearchException;
-
-/**
- * Base class for Jena-related ontology search exceptions.
- */
-class OntologySearchJenaException extends OntologySearchException {
-
- private final JenaException cause;
-
- public OntologySearchJenaException( String message, String query, JenaException cause ) {
- super( message, query, cause );
- this.cause = cause;
- }
-
- @Override
- public JenaException getCause() {
- return cause;
- }
-}
diff --git a/src/ubic/basecode/ontology/jena/OntologyTermImpl.java b/src/ubic/basecode/ontology/jena/OntologyTermImpl.java
index 04e9edb5..fba48075 100644
--- a/src/ubic/basecode/ontology/jena/OntologyTermImpl.java
+++ b/src/ubic/basecode/ontology/jena/OntologyTermImpl.java
@@ -61,12 +61,6 @@ public OntologyTermImpl( OntClass resource, Set additionalRestricti
this.additionalRestrictions = additionalRestrictions;
}
- public OntologyTermImpl( OntClass resource, Set additionalRestrictions, double score ) {
- super( resource, score );
- this.ontResource = resource;
- this.additionalRestrictions = additionalRestrictions;
- }
-
@Override
public Collection getAlternativeIds() {
return getAnnotations( HAS_ALTERNATE_ID ).stream().map( AnnotationProperty::getContents ).collect( Collectors.toSet() );
diff --git a/src/ubic/basecode/ontology/jena/RO.java b/src/ubic/basecode/ontology/jena/RO.java
index 86d5ec73..2c555e13 100644
--- a/src/ubic/basecode/ontology/jena/RO.java
+++ b/src/ubic/basecode/ontology/jena/RO.java
@@ -5,5 +5,33 @@
class RO {
+ private static final String NS = "http://purl.obolibrary.org/obo/";
+
+ private static Property property( String localName ) {
+ return ResourceFactory.createProperty( NS + localName );
+ }
+
+ public static final Property partOf = property( "BFO_0000050" );
+ public static final Property activeIngredientIn = property( "RO_0002249" );
+ public static final Property boundingLayerOf = property( "RO_0002007" );
+ public static final Property branchingPartOf = property( "RO_0002380" );
+ public static final Property determinedBy = property( "RO_0002507" );
+ public static final Property ends = property( "RO_0002229" );
+ public static final Property isSubsequenceOf = property( "RO_0002525" );
+ public static final Property isEndSequenceOf = property( "RO_0002519" );
+ public static final Property isStartSequenceOf = property( "RO_0002517" );
+ public static final Property lumenOf = property( "RO_0002571" );
+ public static final Property luminalSpaceOf = property( "RO_0002572" );
+ public static final Property mainStemOf = property( "RO_0002381" );
+ public static final Property memberOf = property( "RO_0002350" );
+ public static final Property occurrentPartOf = property( "RO_0002012" );
+ public static final Property skeletonOf = property( "RO_0002576" );
+ public static final Property starts = property( "RO_0002223" );
+ public static final Property subclusterOf = property( "RO_0015003" );
+
+ /**
+ * This term is still used in older ontologies.
+ */
+ @Deprecated
public static final Property properPartOf = ResourceFactory.createProperty( "http://www.obofoundry.org/ro/ro.owl#proper_part_of" );
}
diff --git a/src/ubic/basecode/ontology/jena/RestrictionWithOnPropertyFilter.java b/src/ubic/basecode/ontology/jena/RestrictionWithOnPropertyFilter.java
index cb5ed9c7..95b97d1b 100644
--- a/src/ubic/basecode/ontology/jena/RestrictionWithOnPropertyFilter.java
+++ b/src/ubic/basecode/ontology/jena/RestrictionWithOnPropertyFilter.java
@@ -10,9 +10,9 @@
* Filter that retain only the restrictions on any of the given properties.
*/
class RestrictionWithOnPropertyFilter extends Filter {
- private final Set properties;
+ private final Set properties;
- public RestrictionWithOnPropertyFilter( Set properties ) {
+ public RestrictionWithOnPropertyFilter( Set properties ) {
this.properties = properties;
}
diff --git a/src/ubic/basecode/ontology/jena/SearchIndex.java b/src/ubic/basecode/ontology/jena/SearchIndex.java
index 0157263d..7b6a3b73 100644
--- a/src/ubic/basecode/ontology/jena/SearchIndex.java
+++ b/src/ubic/basecode/ontology/jena/SearchIndex.java
@@ -1,74 +1,46 @@
-/*
- * The baseCode project
- *
- * Copyright (c) 2013 University of British Columbia
- *
- * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with
- * the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on
- * an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations under the License.
- */
package ubic.basecode.ontology.jena;
-import com.hp.hpl.jena.util.iterator.Map1Iterator;
-import org.apache.jena.larq.ARQLuceneException;
-import org.apache.jena.larq.HitLARQ;
-import org.apache.jena.larq.IndexLARQ;
-import org.apache.jena.larq.LARQ;
-import org.apache.lucene.analysis.Analyzer;
-import org.apache.lucene.index.IndexReader;
-import org.apache.lucene.index.MultiReader;
-import org.apache.lucene.search.IndexSearcher;
-import org.apache.lucene.search.Query;
-import org.apache.lucene.search.TopDocs;
-
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.Iterator;
-
-/**
- * Customization to deal with MultiReader and 'open' while indexing is going on ...? Might not be needed.
- *
- * @author Paul
- */
-class SearchIndex extends IndexLARQ {
-
- public SearchIndex( MultiReader r, Analyzer a ) {
- super( r, a );
- }
-
- @Override
- public Iterator search( String queryString ) {
- try {
- final IndexSearcher s = getIndexSearcher();
- Query query = getLuceneQueryParser().parse( queryString );
-
- TopDocs topDocs = s.search( query, null, LARQ.NUM_RESULTS );
-
- return new Map1Iterator<>( object -> new HitLARQ( s, object ), Arrays.asList( topDocs.scoreDocs ).iterator() );
- } catch ( Exception e ) {
- throw new ARQLuceneException( "Error during search for '" + queryString + ";", e );
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.util.iterator.ExtendedIterator;
+import ubic.basecode.ontology.search.OntologySearchException;
+
+interface SearchIndex extends AutoCloseable {
+
+ /**
+ * Find RDF nodes matching the given query string.
+ */
+ ExtendedIterator search( OntModel model, String queryString, int maxResults ) throws OntologySearchException;
+
+ /**
+ * Find classes that match the query string.
+ *
+ * @param model that goes with the index
+ * @return Collection of OntologyTerm objects
+ */
+ ExtendedIterator searchClasses( OntModel model, String queryString, int maxResults ) throws OntologySearchException;
+
+ /**
+ * Find individuals that match the query string
+ *
+ * @param model that goes with the index
+ * @return Collection of OntologyTerm objects
+ */
+ ExtendedIterator searchIndividuals( OntModel model, String queryString, int maxResults ) throws OntologySearchException;
+
+ class JenaSearchResult {
+
+ public final Resource result;
+ public final double score;
+
+ JenaSearchResult( Resource result, double score ) {
+ this.result = result;
+ this.score = score;
}
- }
-
- private synchronized IndexSearcher getIndexSearcher() throws IOException {
- if ( !reader.isCurrent() ) {
- // this is the problematic line ... multireader cannot be reopened; was IndexReader newReader =
- // IndexReader.openIfChanged(reader, true) ;
- IndexReader newReader = IndexReader.openIfChanged( reader );
- if ( newReader != null ) {
- reader.close();
- reader = newReader;
- searcher = new IndexSearcher( reader );
- }
+ @Override
+ public String toString() {
+ return String.format( "%s score=%f", result, score );
}
-
- return searcher;
}
-
}
diff --git a/src/ubic/basecode/ontology/jena/package-info.java b/src/ubic/basecode/ontology/jena/package-info.java
index 5d1211e8..a10a5631 100644
--- a/src/ubic/basecode/ontology/jena/package-info.java
+++ b/src/ubic/basecode/ontology/jena/package-info.java
@@ -1,5 +1,5 @@
/**
- *
+ * Implementation of {@link ubic.basecode.ontology.providers.OntologyService} using Apache Jena.
*/
@ParametersAreNonnullByDefault
package ubic.basecode.ontology.jena;
diff --git a/src/ubic/basecode/ontology/model/OntologyResource.java b/src/ubic/basecode/ontology/model/OntologyResource.java
index 2284ebc0..f7fecbb1 100644
--- a/src/ubic/basecode/ontology/model/OntologyResource.java
+++ b/src/ubic/basecode/ontology/model/OntologyResource.java
@@ -23,7 +23,7 @@
/**
* @author pavlidis
*/
-public interface OntologyResource extends Comparable {
+public interface OntologyResource {
/**
* A URI if known, otherwise null.
@@ -52,10 +52,4 @@ public interface OntologyResource extends Comparable {
* Whether the resource is marked as obsolete.
*/
boolean isObsolete();
-
- /**
- * If this is result from a free-text search, a corresponding score, otherwise null.
- */
- @Nullable
- Double getScore();
}
diff --git a/src/ubic/basecode/ontology/model/OntologyTermSimple.java b/src/ubic/basecode/ontology/model/OntologyTermSimple.java
index d22bb703..5aadf4da 100644
--- a/src/ubic/basecode/ontology/model/OntologyTermSimple.java
+++ b/src/ubic/basecode/ontology/model/OntologyTermSimple.java
@@ -17,7 +17,6 @@
import javax.annotation.Nullable;
import java.io.Serializable;
import java.util.Collection;
-import java.util.Comparator;
import java.util.Objects;
/**
@@ -131,17 +130,6 @@ public boolean isObsolete() {
return obsolete;
}
- @Nullable
- @Override
- public Double getScore() {
- return null;
- }
-
- @Override
- public int compareTo( OntologyResource other ) {
- return Objects.compare( getUri(), other.getUri(), Comparator.nullsLast( Comparator.naturalOrder() ) );
- }
-
@Override
public boolean equals( Object obj ) {
if ( this == obj ) return true;
diff --git a/src/ubic/basecode/ontology/providers/AbstractBaseCodeOntologyService.java b/src/ubic/basecode/ontology/providers/AbstractBaseCodeOntologyService.java
new file mode 100644
index 00000000..5c4b0c3b
--- /dev/null
+++ b/src/ubic/basecode/ontology/providers/AbstractBaseCodeOntologyService.java
@@ -0,0 +1,48 @@
+package ubic.basecode.ontology.providers;
+
+import ubic.basecode.util.Configuration;
+
+import javax.annotation.Nullable;
+
+/**
+ * Base class for all ontologies built-in to the baseCode project.
+ *
+ * The ontologies that subclass this will honor settings in the {@code basecode.properties} file for loading and
+ * locating the ontology.
+ *
+ * @author poirigui
+ */
+public abstract class AbstractBaseCodeOntologyService extends AbstractOntologyService {
+
+ private final String name;
+ private final String cacheName;
+
+ /**
+ * Intentionally package-private constructor.
+ */
+ AbstractBaseCodeOntologyService( String name, String cacheName ) {
+ this.name = name;
+ this.cacheName = cacheName;
+ }
+
+ @Override
+ protected String getOntologyName() {
+ return name;
+ }
+
+ @Override
+ protected String getOntologyUrl() {
+ return Configuration.getString( "url." + cacheName );
+ }
+
+ @Override
+ protected boolean isOntologyEnabled() {
+ return Boolean.TRUE.equals( Configuration.getBoolean( "load." + cacheName ) );
+ }
+
+ @Nullable
+ @Override
+ public String getCacheName() {
+ return cacheName;
+ }
+}
diff --git a/src/ubic/basecode/ontology/providers/AbstractOntologyService.java b/src/ubic/basecode/ontology/providers/AbstractOntologyService.java
new file mode 100644
index 00000000..7549a348
--- /dev/null
+++ b/src/ubic/basecode/ontology/providers/AbstractOntologyService.java
@@ -0,0 +1,9 @@
+package ubic.basecode.ontology.providers;
+
+/**
+ * Base class for all ontology services.
+ *
+ * The actual implementation is provided by the {@code ubic.basecode.ontology.jena} package.
+ */
+public abstract class AbstractOntologyService extends ubic.basecode.ontology.jena.AbstractOntologyService {
+}
diff --git a/src/ubic/basecode/ontology/providers/CellLineOntologyService.java b/src/ubic/basecode/ontology/providers/CellLineOntologyService.java
index 9c60ff24..e77be6a9 100644
--- a/src/ubic/basecode/ontology/providers/CellLineOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/CellLineOntologyService.java
@@ -1,8 +1,8 @@
/*
* The baseCode project
- *
+ *
* Copyright (c) 2010 University of British Columbia
- *
+ *
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
@@ -19,26 +19,14 @@
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
/**
- * See http://www.obofoundry.org/cgi-bin/detail.cgi?id=CLO
- *
+ * Cell Line Ontology
+ *
* @author paul
- *
*/
-public class CellLineOntologyService extends AbstractOntologyMemoryBackedService {
-
- private static final String ONTOLOGY_URL = "url.cellLineOntology";
-
- @Override
- protected String getOntologyName() {
- return "cellLineOntology";
- }
+public class CellLineOntologyService extends AbstractBaseCodeOntologyService {
- @Override
- protected String getOntologyUrl() {
- return Configuration.getString( ONTOLOGY_URL );
+ public CellLineOntologyService() {
+ super( "Cell Line Ontology", "cellLineOntology" );
}
}
diff --git a/src/ubic/basecode/ontology/providers/CellTypeOntologyService.java b/src/ubic/basecode/ontology/providers/CellTypeOntologyService.java
index 6ebb09e8..bfbcf55b 100644
--- a/src/ubic/basecode/ontology/providers/CellTypeOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/CellTypeOntologyService.java
@@ -1,8 +1,8 @@
/*
* The baseCode project
- *
+ *
* Copyright (c) 2010 University of British Columbia
- *
+ *
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
@@ -19,26 +19,14 @@
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
/**
- * See http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell
- *
+ * Cell Ontology
+ *
* @author paul
- *
*/
-public class CellTypeOntologyService extends AbstractOntologyMemoryBackedService {
-
- private static final String ONTOLOGY_URL = "url.cellTypeOntology";
-
- @Override
- protected String getOntologyName() {
- return "cellTypeOntology";
- }
+public class CellTypeOntologyService extends AbstractBaseCodeOntologyService {
- @Override
- protected String getOntologyUrl() {
- return Configuration.getString( ONTOLOGY_URL );
+ public CellTypeOntologyService() {
+ super( "Cell Ontology", "cellTypeOntology" );
}
-}
+}
\ No newline at end of file
diff --git a/src/ubic/basecode/ontology/providers/ChebiOntologyService.java b/src/ubic/basecode/ontology/providers/ChebiOntologyService.java
index d6659c6f..59b87ee2 100644
--- a/src/ubic/basecode/ontology/providers/ChebiOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/ChebiOntologyService.java
@@ -1,8 +1,8 @@
/*
* The basecode project
- *
+ *
* Copyright (c) 2007-2019 University of British Columbia
- *
+ *
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
@@ -19,27 +19,14 @@
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
/**
- * Loads the CHEBI Ontology at startup in its own thread. Controlled in build.properties by load.chebiOntology
- *
+ * Chemical Entities of Biological Interest
+ *
* @author klc
- *
*/
-public class ChebiOntologyService extends AbstractOntologyMemoryBackedService {
+public class ChebiOntologyService extends AbstractBaseCodeOntologyService {
- private static final String CHEBI_ONTOLOGY_URL = "url.chebiOntology";
-
- @Override
- protected String getOntologyName() {
- return "chebiOntology";
- }
-
- @Override
- protected String getOntologyUrl() {
- return Configuration.getString( CHEBI_ONTOLOGY_URL );
+ public ChebiOntologyService() {
+ super( "CHEBI", "chebiOntology" );
}
-
}
diff --git a/src/ubic/basecode/ontology/providers/DiseaseOntologyService.java b/src/ubic/basecode/ontology/providers/DiseaseOntologyService.java
index 7ade3f5b..11ec6808 100644
--- a/src/ubic/basecode/ontology/providers/DiseaseOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/DiseaseOntologyService.java
@@ -1,8 +1,8 @@
/*
* The Gemma21 project
- *
+ *
* Copyright (c) 2007-2019 University of British Columbia
- *
+ *
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
@@ -18,26 +18,16 @@
*/
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
/**
* Holds a copy of the Disease Ontology.
- *
+ *
* @author klc
+ * @deprecated use MONDO instead
*/
-public class DiseaseOntologyService extends AbstractOntologyMemoryBackedService {
+@Deprecated
+public class DiseaseOntologyService extends AbstractBaseCodeOntologyService {
- private static final String DISEASE_ONTOLOGY_URL = "url.diseaseOntology";
-
- @Override
- protected String getOntologyName() {
- return "diseaseOntology";
- }
-
- @Override
- protected String getOntologyUrl() {
- return Configuration.getString( DISEASE_ONTOLOGY_URL );
+ public DiseaseOntologyService() {
+ super( "Disease Ontology", "diseaseOntology" );
}
-
}
diff --git a/src/ubic/basecode/ontology/providers/ExperimentalFactorOntologyService.java b/src/ubic/basecode/ontology/providers/ExperimentalFactorOntologyService.java
index cdde9564..3ebc37a0 100644
--- a/src/ubic/basecode/ontology/providers/ExperimentalFactorOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/ExperimentalFactorOntologyService.java
@@ -1,38 +1,34 @@
/*
* The baseCode project
- *
+ *
* Copyright (c) 2012 University of British Columbia
- *
+ *
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on
* an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the
* specific language governing permissions and limitations under the License.
*/
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
import ubic.basecode.util.Configuration;
/**
+ * Experimental Factor Ontology
+ *
* @author Paul
- *
*/
-public class ExperimentalFactorOntologyService extends AbstractOntologyMemoryBackedService {
+public class ExperimentalFactorOntologyService extends AbstractBaseCodeOntologyService {
- private static final String EF_ONTOLOGY_URL = "url.efOntology";
-
- @Override
- protected String getOntologyName() {
- return "experimentalFactorOntology";
+ public ExperimentalFactorOntologyService() {
+ super( "Experimental Factor Ontology", "experimentalFactorOntology" );
}
@Override
protected String getOntologyUrl() {
- return Configuration.getString( EF_ONTOLOGY_URL );
+ return Configuration.getString( "url.efOntology" );
}
-
}
diff --git a/src/ubic/basecode/ontology/providers/FMAOntologyService.java b/src/ubic/basecode/ontology/providers/FMAOntologyService.java
index 1f80f650..b12b43d8 100644
--- a/src/ubic/basecode/ontology/providers/FMAOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/FMAOntologyService.java
@@ -1,8 +1,8 @@
/*
* The Gemma21 project
- *
+ *
* Copyright (c) 2007-2019 University of British Columbia
- *
+ *
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
@@ -19,27 +19,16 @@
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
/**
- * Holds a copy of the FMA Ontology on disk. This gets loaded on startup.
- *
+ * Foundational Model of Anatomy Ontology (subset)
+ *
* @author klc
- *
+ * @deprecated this ontology is inactive, use UBERON instead
*/
-public class FMAOntologyService extends AbstractOntologyMemoryBackedService {
+@Deprecated
+public class FMAOntologyService extends AbstractBaseCodeOntologyService {
- private static final String FMA_ONTOLOGY_URL = "url.fmaOntology";
-
- @Override
- protected String getOntologyName() {
- return "fmaOntology";
- }
-
- @Override
- protected String getOntologyUrl() {
- return Configuration.getString( FMA_ONTOLOGY_URL );
+ public FMAOntologyService() {
+ super( "Foundational Model of Anatomy Ontology (subset)", "fmaOntology" );
}
-
}
diff --git a/src/ubic/basecode/ontology/providers/GenericOntologyService.java b/src/ubic/basecode/ontology/providers/GenericOntologyService.java
index 2747c235..d83762ee 100644
--- a/src/ubic/basecode/ontology/providers/GenericOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/GenericOntologyService.java
@@ -14,31 +14,47 @@
*/
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
+import org.apache.commons.lang3.StringUtils;
+
+import javax.annotation.Nullable;
/**
- * A way to create ad hoc ontology services (in memory) for testing
+ * A way to create ad-hoc in-memory ontology services.
*
* @author Paul
*/
-public class GenericOntologyService extends AbstractOntologyMemoryBackedService {
+public class GenericOntologyService extends AbstractOntologyService {
private final String url;
private final String name;
- private final boolean cache;
+ @Nullable
+ private final String cacheName;
+
+ public GenericOntologyService( String name, String url, @Nullable String cacheName ) {
+ this.name = name;
+ this.url = url;
+ this.cacheName = cacheName;
+ }
public GenericOntologyService( String name, String url ) {
- this( name, url, false );
+ this( name, url, null );
}
+ /**
+ * @deprecated use {@link #GenericOntologyService(String, String, String)} with an explicit cache name instead
+ */
+ @Deprecated
public GenericOntologyService( String name, String url, boolean cache ) {
- this( name, url, cache, true );
+ this( name, url, cache ? StringUtils.deleteWhitespace( name ) : null );
}
+ /**
+ * @deprecated use {@link #GenericOntologyService(String, String, String)} with an explicit cache name instead and
+ * {@link #setProcessImports(boolean)}
+ */
+ @Deprecated
public GenericOntologyService( String name, String url, boolean cache, boolean processImports ) {
- this.name = name;
- this.url = url;
- this.cache = cache;
+ this( name, url, cache );
setProcessImports( processImports );
}
@@ -53,7 +69,13 @@ protected String getOntologyUrl() {
}
@Override
+ protected boolean isOntologyEnabled() {
+ return true;
+ }
+
+ @Override
+ @Nullable
protected String getCacheName() {
- return this.cache ? this.name : null;
+ return cacheName;
}
}
diff --git a/src/ubic/basecode/ontology/providers/HumanDevelopmentOntologyService.java b/src/ubic/basecode/ontology/providers/HumanDevelopmentOntologyService.java
index 171a029f..8f69b197 100644
--- a/src/ubic/basecode/ontology/providers/HumanDevelopmentOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/HumanDevelopmentOntologyService.java
@@ -1,8 +1,8 @@
/*
* The baseCode project
- *
+ *
* Copyright (c) 2010 University of British Columbia
- *
+ *
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
@@ -19,25 +19,16 @@
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
/**
+ * Human developmental anatomy, abstract
+ *
* @author paul
- *
+ * @deprecated this ontology was last updated in unmaintained since 2013
*/
-public class HumanDevelopmentOntologyService extends AbstractOntologyMemoryBackedService {
+@Deprecated
+public class HumanDevelopmentOntologyService extends AbstractBaseCodeOntologyService {
- private static final String ONTOLOGY_URL = "url.humanDevelOntology";
-
- @Override
- protected String getOntologyName() {
- return "humanDevelOntology";
- }
-
- @Override
- protected String getOntologyUrl() {
- return Configuration.getString( ONTOLOGY_URL );
+ public HumanDevelopmentOntologyService() {
+ super( "Human Development Ontology", "humanDevelOntology" );
}
-
}
diff --git a/src/ubic/basecode/ontology/providers/HumanPhenotypeOntologyService.java b/src/ubic/basecode/ontology/providers/HumanPhenotypeOntologyService.java
index 2b7a201d..b8b24e65 100644
--- a/src/ubic/basecode/ontology/providers/HumanPhenotypeOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/HumanPhenotypeOntologyService.java
@@ -1,8 +1,8 @@
/*
* The baseCode project
- *
+ *
* Copyright (c) 2011 University of British Columbia
- *
+ *
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
@@ -19,27 +19,14 @@
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
/**
- * See http://bioportal.bioontology.org/ontologies/45774?p=terms&conceptid=HP%3A0001264 for example.
- *
+ * Human Phenotype Ontology
+ *
* @author paul
- *
*/
-public class HumanPhenotypeOntologyService extends AbstractOntologyMemoryBackedService {
+public class HumanPhenotypeOntologyService extends AbstractBaseCodeOntologyService {
- private static final String ONTOLOGY_URL = "url.humanPhenotypeOntology";
-
- @Override
- protected String getOntologyName() {
- return "humanPhenotypeOntology";
- }
-
- @Override
- protected String getOntologyUrl() {
- return Configuration.getString( ONTOLOGY_URL );
+ public HumanPhenotypeOntologyService() {
+ super( "Human Phenotype Ontology", "humanPhenotypeOntology" );
}
-
}
diff --git a/src/ubic/basecode/ontology/providers/MammalianPhenotypeOntologyService.java b/src/ubic/basecode/ontology/providers/MammalianPhenotypeOntologyService.java
index ffa43d00..9acb5d6f 100644
--- a/src/ubic/basecode/ontology/providers/MammalianPhenotypeOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/MammalianPhenotypeOntologyService.java
@@ -1,8 +1,8 @@
/*
* The basecode project
- *
+ *
* Copyright (c) 2007-2019 University of British Columbia
- *
+ *
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
@@ -19,27 +19,14 @@
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
/**
+ * Mammalian Phenotype Ontology
+ *
* @author klc
- *
*/
-public class MammalianPhenotypeOntologyService extends AbstractOntologyMemoryBackedService {
-
- private static final String ONTOLOGY_URL = "url.mammalPhenotypeOntology";
+public class MammalianPhenotypeOntologyService extends AbstractBaseCodeOntologyService {
- @Override
- protected String getOntologyName() {
-
- return "mammalPhenotypeOntology";
+ public MammalianPhenotypeOntologyService() {
+ super( "Mammalian Phenotype Ontology", "mammalPhenotypeOntology" );
}
-
- @Override
- protected String getOntologyUrl() {
- return Configuration.getString( ONTOLOGY_URL );
-
- }
-
}
diff --git a/src/ubic/basecode/ontology/providers/MedicOntologyService.java b/src/ubic/basecode/ontology/providers/MedicOntologyService.java
index 96d56e49..8a4d9820 100644
--- a/src/ubic/basecode/ontology/providers/MedicOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/MedicOntologyService.java
@@ -18,7 +18,6 @@
*/
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
import ubic.basecode.ontology.model.OntologyModel;
import java.io.IOException;
@@ -29,21 +28,21 @@
* MEDIC ONTOLOGY USED BY PHENOCARTA, its represents MESH terms as a tree so with can use the parent structure that a
* normal mesh term doesnt have
*
- * MEDIC comes from the CTD folks. See http://ctd.mdibl.org/voc.go?type=disease. Unfortunately I do not know where our
+ * MEDIC comes from the CTD folks. See .... Unfortunately I do not know where our
* medic.owl file came from (PP)
*
* @author Nicolas
*/
-public class MedicOntologyService extends AbstractOntologyMemoryBackedService {
+@Deprecated
+public class MedicOntologyService extends AbstractBaseCodeOntologyService {
/**
* FIXME this shouldn't be hard-coded like this, we should load it like any other ontology service.
*/
private static final String MEDIC_ONTOLOGY_FILE = "/data/loader/ontology/medic.owl.gz";
- @Override
- protected String getOntologyName() {
- return "medicOntology";
+ public MedicOntologyService() {
+ super( "Medic Ontology", "medicOntology" );
}
@Override
diff --git a/src/ubic/basecode/ontology/providers/MouseDevelopmentOntologyService.java b/src/ubic/basecode/ontology/providers/MouseDevelopmentOntologyService.java
index 2dcf1826..cbcc54f0 100644
--- a/src/ubic/basecode/ontology/providers/MouseDevelopmentOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/MouseDevelopmentOntologyService.java
@@ -1,8 +1,8 @@
/*
* The baseCode project
- *
+ *
* Copyright (c) 2010 University of British Columbia
- *
+ *
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
@@ -19,25 +19,14 @@
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
/**
+ * Mouse Developmental Anatomy Ontology
+ *
* @author paul
- *
*/
-public class MouseDevelopmentOntologyService extends AbstractOntologyMemoryBackedService {
+public class MouseDevelopmentOntologyService extends AbstractBaseCodeOntologyService {
- private static final String ONTOLOGY_URL = "url.mouseDevelOntology";
-
- @Override
- protected String getOntologyName() {
- return "mouseDevelOntology";
- }
-
- @Override
- protected String getOntologyUrl() {
- return Configuration.getString( ONTOLOGY_URL );
+ public MouseDevelopmentOntologyService() {
+ super( "Mouse Development Anatomy Ontology", "mouseDevelOntology" );
}
-
}
diff --git a/src/ubic/basecode/ontology/providers/NIFSTDOntologyService.java b/src/ubic/basecode/ontology/providers/NIFSTDOntologyService.java
index ad2ec55a..1b133b10 100644
--- a/src/ubic/basecode/ontology/providers/NIFSTDOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/NIFSTDOntologyService.java
@@ -14,7 +14,6 @@
*/
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
import ubic.basecode.ontology.model.OntologyModel;
import java.io.IOException;
@@ -24,19 +23,16 @@
/**
* @author paul
*/
-public class NIFSTDOntologyService extends AbstractOntologyMemoryBackedService {
+@Deprecated
+public class NIFSTDOntologyService extends AbstractBaseCodeOntologyService {
private static final String NIFSTD_ONTOLOGY_FILE = "/data/loader/ontology/nif-gemma.owl.gz";
public NIFSTDOntologyService() {
+ super( "NISFTD", "nisftdOntology" );
setProcessImports( false );
}
- @Override
- protected String getOntologyName() {
- return "nifstdOntology";
- }
-
@Override
protected String getOntologyUrl() {
return "classpath:" + NIFSTD_ONTOLOGY_FILE;
diff --git a/src/ubic/basecode/ontology/providers/ObiService.java b/src/ubic/basecode/ontology/providers/ObiService.java
index f8e4ce9f..910b9ed4 100644
--- a/src/ubic/basecode/ontology/providers/ObiService.java
+++ b/src/ubic/basecode/ontology/providers/ObiService.java
@@ -1,8 +1,8 @@
/*
* The baseCode project
- *
+ *
* Copyright (c) 2010 University of British Columbia
- *
+ *
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
@@ -19,25 +19,14 @@
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
/**
+ * Ontology for Biomedical Investigations
+ *
* @author paul
- *
*/
-public class ObiService extends AbstractOntologyMemoryBackedService {
+public class ObiService extends AbstractBaseCodeOntologyService {
- private static final String ONTOLOGY_URL = "url.obiOntology";
-
- @Override
- protected String getOntologyName() {
- return "obiOntology";
- }
-
- @Override
- protected String getOntologyUrl() {
- return Configuration.getString( ONTOLOGY_URL );
+ public ObiService() {
+ super( "Ontology for Biomedical Investigations", "obiOntology" );
}
-
}
diff --git a/src/ubic/basecode/ontology/providers/OntologyService.java b/src/ubic/basecode/ontology/providers/OntologyService.java
index fb8970ce..8cc3ccd1 100644
--- a/src/ubic/basecode/ontology/providers/OntologyService.java
+++ b/src/ubic/basecode/ontology/providers/OntologyService.java
@@ -4,6 +4,7 @@
import ubic.basecode.ontology.model.OntologyResource;
import ubic.basecode.ontology.model.OntologyTerm;
import ubic.basecode.ontology.search.OntologySearchException;
+import ubic.basecode.ontology.search.OntologySearchResult;
import javax.annotation.Nullable;
import java.io.InputStream;
@@ -116,9 +117,9 @@ enum InferenceMode {
*
* Search is enabled by default.
*
- * @see #findTerm(String, boolean)
- * @see #findIndividuals(String, boolean)
- * @see #findResources(String, boolean)
+ * @see #findTerm(String, int, boolean)
+ * @see #findIndividuals(String, int, boolean)
+ * @see #findResources(String, int, boolean)
*/
boolean isSearchEnabled();
@@ -129,6 +130,19 @@ enum InferenceMode {
*/
void setSearchEnabled( boolean searchEnabled );
+ /**
+ * Obtain the words that should be excluded from stemming.
+ *
+ * By default, all words are subject to stemming. The exact implementation of stemming depends on the actual search
+ * implementation.
+ */
+ Set getExcludedWordsFromStemming();
+
+ /**
+ * Set words that should be excluded from stemming when searching.
+ */
+ void setExcludedWordsFromStemming( Set excludedWordsFromStemming );
+
/**
* Obtain the URIs used as additional properties when inferring parents and children.
*
@@ -169,8 +183,8 @@ enum InferenceMode {
*
* Obsolete terms are filtered out.
*/
- default Collection findIndividuals( String search ) throws OntologySearchException {
- return findIndividuals( search, false );
+ default Collection> findIndividuals( String search, int maxResults ) throws OntologySearchException {
+ return findIndividuals( search, maxResults, false );
}
/**
@@ -179,7 +193,7 @@ default Collection findIndividuals( String search ) throws O
* @param search search query
* @param keepObsoletes retain obsolete terms
*/
- Collection findIndividuals( String search, boolean keepObsoletes ) throws OntologySearchException;
+ Set> findIndividuals( String search, int maxResults, boolean keepObsoletes ) throws OntologySearchException;
/**
* Looks for any resources (terms or individuals) that match the given search string
@@ -189,8 +203,8 @@ default Collection findIndividuals( String search ) throws O
* @return results, or an empty collection if the results are empty OR the ontology is not available to be
* searched.
*/
- default Collection findResources( String searchString ) throws OntologySearchException {
- return findResources( searchString, false );
+ default Collection> findResources( String searchString, int maxResults ) throws OntologySearchException {
+ return findResources( searchString, maxResults, false );
}
/**
@@ -199,15 +213,15 @@ default Collection findResources( String searchString ) throws
* @param search search query
* @param keepObsoletes retain obsolete terms
*/
- Collection findResources( String search, boolean keepObsoletes ) throws OntologySearchException;
+ Collection> findResources( String search, int maxResults, boolean keepObsoletes ) throws OntologySearchException;
/**
* Looks for any terms that match the given search string.
*
* Obsolete terms are filtered out.
*/
- default Collection findTerm( String search ) throws OntologySearchException {
- return findTerm( search, false );
+ default Collection> findTerm( String search, int maxResults ) throws OntologySearchException {
+ return findTerm( search, maxResults, false );
}
@@ -217,7 +231,7 @@ default Collection findTerm( String search ) throws OntologySearch
* @param search search query
* @param keepObsoletes retain obsolete terms
*/
- Collection findTerm( String search, boolean keepObsoletes ) throws OntologySearchException;
+ Collection> findTerm( String search, int maxResults, boolean keepObsoletes ) throws OntologySearchException;
/**
* Find a term using an alternative ID.
@@ -288,7 +302,6 @@ default Set getChildren( Collection terms, boolean d
*/
Set getChildren( Collection terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes );
-
/**
* Check if this ontology is enabled.
*/
diff --git a/src/ubic/basecode/ontology/providers/SequenceOntologyService.java b/src/ubic/basecode/ontology/providers/SequenceOntologyService.java
index 6aa71d33..55b707b1 100644
--- a/src/ubic/basecode/ontology/providers/SequenceOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/SequenceOntologyService.java
@@ -1,8 +1,8 @@
/*
* The baseCode project
- *
+ *
* Copyright (c) 2013 University of British Columbia
- *
+ *
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
@@ -19,27 +19,14 @@
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
/**
- * Support for the Sequence Ontology
- *
+ * Sequence types and features ontology
+ *
* @author Paul
- *
*/
-public class SequenceOntologyService extends AbstractOntologyMemoryBackedService {
+public class SequenceOntologyService extends AbstractBaseCodeOntologyService {
- private static final String SO_ONTOLOGY_URL = "url.seqOntology";
-
- @Override
- protected String getOntologyName() {
- return "seqOntology";
- }
-
- @Override
- protected String getOntologyUrl() {
- return Configuration.getString( SO_ONTOLOGY_URL );
+ public SequenceOntologyService() {
+ super( "Sequence types and features ontology", "seqOntology" );
}
-
}
diff --git a/src/ubic/basecode/ontology/providers/UberonOntologyService.java b/src/ubic/basecode/ontology/providers/UberonOntologyService.java
index 51967a98..d9e2c6e1 100644
--- a/src/ubic/basecode/ontology/providers/UberonOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/UberonOntologyService.java
@@ -1,8 +1,8 @@
/*
* The baseCode project
- *
+ *
* Copyright (c) 2015 University of British Columbia
- *
+ *
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
@@ -19,27 +19,14 @@
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
/**
- * Uberon
- *
+ * Uberon multi-species anatomy ontology
+ *
* @author paul
- *
*/
-public class UberonOntologyService extends AbstractOntologyMemoryBackedService {
+public class UberonOntologyService extends AbstractBaseCodeOntologyService {
- private static final String ONTOLOGY_URL = "url.uberonOntology";
-
- @Override
- protected String getOntologyName() {
- return "uberonOntology";
- }
-
- @Override
- protected String getOntologyUrl() {
- return Configuration.getString( ONTOLOGY_URL );
+ public UberonOntologyService() {
+ super( "Uberon multi-species anatomy ontology", "uberonOntology" );
}
-
}
diff --git a/src/ubic/basecode/ontology/providers/UnitsOntologyService.java b/src/ubic/basecode/ontology/providers/UnitsOntologyService.java
index ed1df01c..1670b011 100644
--- a/src/ubic/basecode/ontology/providers/UnitsOntologyService.java
+++ b/src/ubic/basecode/ontology/providers/UnitsOntologyService.java
@@ -1,8 +1,8 @@
/*
* The baseCode project
- *
+ *
* Copyright (c) 2013 University of British Columbia
- *
+ *
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
@@ -19,27 +19,14 @@
package ubic.basecode.ontology.providers;
-import ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService;
-import ubic.basecode.util.Configuration;
-
/**
- * Support for the units ontology
- *
+ * Units of measurement ontology
+ *
* @author Paul
- *
*/
-public class UnitsOntologyService extends AbstractOntologyMemoryBackedService {
+public class UnitsOntologyService extends AbstractBaseCodeOntologyService {
- private static final String UNITs_ONTOLOGY_URL = "url.unitsOntology";
-
- @Override
- protected String getOntologyName() {
- return "unitsOntology";
- }
-
- @Override
- protected String getOntologyUrl() {
- return Configuration.getString( UNITs_ONTOLOGY_URL );
+ public UnitsOntologyService() {
+ super( "Units of measurement ontology", "unitsOntology" );
}
-
}
diff --git a/src/ubic/basecode/ontology/providers/package-info.java b/src/ubic/basecode/ontology/providers/package-info.java
index 46d274b3..c3735344 100644
--- a/src/ubic/basecode/ontology/providers/package-info.java
+++ b/src/ubic/basecode/ontology/providers/package-info.java
@@ -1,5 +1,11 @@
/**
+ * This package contains baseCode built-in ontologies and a {@link ubic.basecode.ontology.providers.GenericOntologyService}
+ * to implement your own ontologies.
*
+ * @author klc
+ * @author nicolas
+ * @author paul
+ * @author poirigui
*/
@ParametersAreNonnullByDefault
package ubic.basecode.ontology.providers;
diff --git a/src/ubic/basecode/ontology/search/OntologySearch.java b/src/ubic/basecode/ontology/search/OntologySearch.java
deleted file mode 100644
index bf16d97f..00000000
--- a/src/ubic/basecode/ontology/search/OntologySearch.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package ubic.basecode.ontology.search;
-
-import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.text.StringEscapeUtils;
-
-public class OntologySearch {
-
- // Lucene cannot properly parse these characters... gives a query parse error.
- // OntologyTerms don't contain them anyway
- private final static char[] INVALID_CHARS = {':', '(', ')', '?', '^', '[', ']', '{', '}', '!', '~', '"', '\''};
-
- /**
- * Will remove characters that jena is unable to parse. Will also escape and remove leading and trailing white space
- * (which also causes jena to die)
- *
- * @param toStrip the string to clean
- * @return
- */
- public static String stripInvalidCharacters( String toStrip ) {
- String result = StringUtils.strip( toStrip );
- for ( char badChar : INVALID_CHARS ) {
- result = StringUtils.remove( result, badChar );
- }
- /*
- * Queries cannot start with '*' or ?
- */
- result = result.replaceAll( "^\\**", "" );
- result = result.replaceAll( "^\\?*", "" );
-
- return StringEscapeUtils.escapeJava( result ).trim();
- }
-}
diff --git a/src/ubic/basecode/ontology/search/OntologySearchResult.java b/src/ubic/basecode/ontology/search/OntologySearchResult.java
new file mode 100644
index 00000000..f50af3e5
--- /dev/null
+++ b/src/ubic/basecode/ontology/search/OntologySearchResult.java
@@ -0,0 +1,51 @@
+package ubic.basecode.ontology.search;
+
+import ubic.basecode.ontology.model.OntologyResource;
+
+import java.util.Comparator;
+import java.util.Objects;
+
+/**
+ * Represents a search result from an ontology.
+ *
+ * @author poirigui
+ */
+public class OntologySearchResult implements Comparator> {
+
+ private final T result;
+ private final double score;
+
+ public OntologySearchResult( T result, double score ) {
+ this.result = result;
+ this.score = score;
+ }
+
+ public T getResult() {
+ return result;
+ }
+
+ public double getScore() {
+ return score;
+ }
+
+ @Override
+ public int hashCode() {
+ return Objects.hash( result );
+ }
+
+ @Override
+ public boolean equals( Object obj ) {
+ if ( this == obj ) {
+ return true;
+ }
+ if ( !( obj instanceof OntologySearchResult ) ) {
+ return false;
+ }
+ return Objects.equals( result, ( ( OntologySearchResult ) obj ).result );
+ }
+
+ @Override
+ public int compare( OntologySearchResult searchResult, OntologySearchResult t1 ) {
+ return Double.compare( searchResult.score, t1.score );
+ }
+}
diff --git a/src/ubic/basecode/util/Configuration.java b/src/ubic/basecode/util/Configuration.java
index 3f5c030b..19641797 100644
--- a/src/ubic/basecode/util/Configuration.java
+++ b/src/ubic/basecode/util/Configuration.java
@@ -18,112 +18,95 @@
*/
package ubic.basecode.util;
-import java.util.Iterator;
-
-import org.apache.commons.configuration2.CompositeConfiguration;
-import org.apache.commons.configuration2.PropertiesConfiguration;
-import org.apache.commons.configuration2.SystemConfiguration;
-import org.apache.commons.configuration2.ex.ConfigurationException;
-import org.apache.commons.configuration2.io.FileHandler;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import javax.annotation.Nullable;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Properties;
+
/**
* Configuration of ontology services and other things.
+ *
+ * Configurations are retrieved from three locations: properties set at runtime with {@link #setString(String, String)},
+ * system properties and a default properties file named {@code basecode.properties} at the root of the classpath in
+ * that order.
+ *
+ * Properties set via system properties must be prefixed with {@code basecode.} to be considered.
+ *
+ * Properties set at runtime can be reset with {@link #reset()} and {@link #reset(String)}.
*
* @author paul
- *
*/
public class Configuration {
- private static CompositeConfiguration config;
-
- /**
- * Name of the resource containing defaults
- */
- private static final String DEFAULT_CONFIGURATION = "ontology.properties";
-
- private static Logger log = LoggerFactory.getLogger( Configuration.class );
+ private static final Logger log = LoggerFactory.getLogger( Configuration.class );
- /**
- * The name of the file users can use to customize.
- */
- private static final String USER_CONFIGURATION = "basecode.properties";
+ private static final String SYSTEM_PROPERTY_PREFIX = "basecode.";
+ private static final Properties defaultProps = new Properties();
+ private static final Properties props = new Properties();
static {
-
- config = new CompositeConfiguration();
- config.addConfiguration( new SystemConfiguration() );
-
- /*
- * the order matters - first come, first serve. Items added later do not overwrite items defined earlier. Thus
- * the user configuration has to be listed first.
- */
-
- try {
- // purely for backwards compatibility, if the user hasn't set up ontology.properties.
- PropertiesConfiguration pc = new PropertiesConfiguration();
- FileHandler handler = new FileHandler( pc );
- handler.setFileName( "Gemma.properties" );
- handler.load();
- config.addConfiguration( pc );
- } catch ( ConfigurationException e ) {
+ try ( InputStream is = Configuration.class.getResourceAsStream( "/basecode.properties" ) ) {
+ if ( is != null ) {
+ defaultProps.load( is );
+ } else {
+ log.warn( "No basecode.properties was found in the classpath, only system and manually set properties will be considered." );
+ }
+ } catch ( IOException e ) {
+ throw new RuntimeException( e );
}
+ }
- try {
- PropertiesConfiguration pc = new PropertiesConfiguration();
- FileHandler handler = new FileHandler( pc );
- handler.setFileName( USER_CONFIGURATION );
- handler.load();
- config.addConfiguration( pc );
- } catch ( ConfigurationException e ) {
+ /**
+ * Obtain a configuration value by key.
+ */
+ @Nullable
+ public static String getString( String key ) {
+ String val = props.getProperty( key );
+ if ( val == null ) {
+ val = System.getProperty( SYSTEM_PROPERTY_PREFIX + key );
}
-
- try {
- PropertiesConfiguration pc = new PropertiesConfiguration();
- FileHandler handler = new FileHandler( pc );
- handler.setFileName( DEFAULT_CONFIGURATION );
- handler.load();
- config.addConfiguration( pc );
- } catch ( ConfigurationException e ) {
- log.error( DEFAULT_CONFIGURATION + " is missing, ontology loading may fail" );
+ if ( val == null ) {
+ val = defaultProps.getProperty( key );
}
+ return val;
+ }
- // step through the result and do a final round of variable substitution
- for ( Iterator it = config.getKeys(); it.hasNext(); ) {
- String key = it.next();
- String property = config.getString( key );
- if ( property != null && property.startsWith( "${" ) && property.endsWith( "}" ) ) {
- String keyToSubstitute = property.substring( 2, property.length() - 1 );
- String valueToSubstitute = config.getString( keyToSubstitute );
- log.debug( key + "=" + property + " -> " + valueToSubstitute );
- config.setProperty( key, valueToSubstitute );
- }
+ /**
+ * Obtain a boolean configuration value by key.
+ *
+ * @see Boolean#parseBoolean(String)
+ */
+ @Nullable
+ public static Boolean getBoolean( String key ) {
+ String val = getString( key );
+ if ( val != null ) {
+ return Boolean.parseBoolean( val );
+ } else {
+ return null;
}
-
}
/**
- * @param key
- * @return
+ * Set a configuration by key.
*/
- public static boolean getBoolean( String key ) {
- return config.getBoolean( key, false );
+ public static void setString( String key, String value ) {
+ props.setProperty( key, value );
}
/**
- * @param key
- * @return
+ * Reset all configurations set at runtime.
*/
- public static String getString( String key ) {
- return config.getString( key );
+ public static void reset() {
+ props.clear();
}
/**
- * @param key
- * @return
+ * Reset a specific configuration by key.
*/
- public static void setString( String key, Object value ) {
- config.setProperty( key, value );
+ public static void reset( String key ) {
+ props.remove( key );
}
}
diff --git a/src/ubic/basecode/util/r/AbstractRClient.java b/src/ubic/basecode/util/r/AbstractRClient.java
index 65efc7b1..645659d9 100644
--- a/src/ubic/basecode/util/r/AbstractRClient.java
+++ b/src/ubic/basecode/util/r/AbstractRClient.java
@@ -622,7 +622,7 @@ public List listEval( Class listEntryType, String command ) {
public boolean loadLibrary( String libraryName ) {
try {
- String userLibPath = Configuration.getString( "basecode.rlibpath" );
+ String userLibPath = Configuration.getString( "rlibpath" );
if ( StringUtils.isNotBlank( userLibPath ) ) {
voidEval( ".libPaths(" + userLibPath + ")" );
}
diff --git a/src/ubic/basecode/util/r/RServeClient.java b/src/ubic/basecode/util/r/RServeClient.java
index 0f823515..7fe5f4d9 100644
--- a/src/ubic/basecode/util/r/RServeClient.java
+++ b/src/ubic/basecode/util/r/RServeClient.java
@@ -18,15 +18,6 @@
*/
package ubic.basecode.util.r;
-import java.io.File;
-import java.io.IOException;
-import java.net.URL;
-import java.util.Iterator;
-import java.util.List;
-
-import org.apache.commons.configuration2.PropertiesConfiguration;
-import org.apache.commons.configuration2.ex.ConfigurationException;
-import org.apache.commons.configuration2.io.FileHandler;
import org.apache.commons.lang3.StringUtils;
import org.rosuda.REngine.REXP;
import org.rosuda.REngine.REXPMismatchException;
@@ -34,10 +25,14 @@
import org.rosuda.REngine.RList;
import org.rosuda.REngine.Rserve.RConnection;
import org.rosuda.REngine.Rserve.RserveException;
-
import ubic.basecode.dataStructure.matrix.DenseDoubleMatrix;
import ubic.basecode.dataStructure.matrix.DoubleMatrix;
-import ubic.basecode.util.ConfigUtils;
+import ubic.basecode.util.Configuration;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Iterator;
+import java.util.List;
/**
* @author pavlidis
@@ -56,24 +51,8 @@ public class RServeClient extends AbstractRClient {
private final static String os = System.getProperty( "os.name" ).toLowerCase();
- /**
- * @return
- * @throws ConfigurationException
- */
- protected static String findRserveCommand() throws ConfigurationException {
- URL userSpecificConfigFileLocation = ConfigUtils.locate( "local.properties" );
-
- PropertiesConfiguration userConfig = null;
- if ( userSpecificConfigFileLocation != null ) {
- userConfig = new PropertiesConfiguration();
- FileHandler handler = new FileHandler( userConfig );
- handler.setFileName( "local.properties" );
- handler.load();
- }
- String rserveExecutable = null;
- if ( userConfig != null ) {
- rserveExecutable = userConfig.getString( "rserve.start.command" );
- }
+ protected static String findRserveCommand() {
+ String rserveExecutable = Configuration.getString( "rserve.start.command" );
if ( StringUtils.isBlank( rserveExecutable ) ) {
log.info( "Rserve command not configured? Trying fallbacks" );
if ( os.startsWith( "windows" ) ) { // lower cased
diff --git a/test/ubic/basecode/ontology/AbstractOntologyTest.java b/test/ubic/basecode/ontology/AbstractOntologyTest.java
index b9eb42c4..8face625 100644
--- a/test/ubic/basecode/ontology/AbstractOntologyTest.java
+++ b/test/ubic/basecode/ontology/AbstractOntologyTest.java
@@ -17,12 +17,9 @@
public class AbstractOntologyTest {
protected static Path tempDir;
- private static String prevCacheDir, prevIndexDir;
@BeforeClass
public static void setUpOntologyCacheDir() throws IOException {
- prevCacheDir = Configuration.getString( "ontology.cache.dir" );
- prevIndexDir = Configuration.getString( "ontology.index.dir" );
tempDir = Files.createTempDirectory( "baseCode" );
Configuration.setString( "ontology.cache.dir", tempDir.resolve( "ontologyCache" ).toAbsolutePath().toString() );
Configuration.setString( "ontology.index.dir", tempDir.resolve( "searchIndices" ).toAbsolutePath().toString() );
@@ -33,8 +30,8 @@ public static void clearOntologyCacheDir() throws IOException {
try {
PathUtils.deleteDirectory( tempDir );
} finally {
- Configuration.setString( "ontology.cache.dir", prevCacheDir );
- Configuration.setString( "ontology.index.dir", prevIndexDir );
+ Configuration.reset( "ontology.cache.dir" );
+ Configuration.reset( "ontology.index.dir" );
}
}
}
diff --git a/test/ubic/basecode/ontology/jena/OntologyLoaderTest.java b/test/ubic/basecode/ontology/jena/OntologyLoaderTest.java
index 7430ce0c..5260bdbf 100644
--- a/test/ubic/basecode/ontology/jena/OntologyLoaderTest.java
+++ b/test/ubic/basecode/ontology/jena/OntologyLoaderTest.java
@@ -19,6 +19,7 @@
import ubic.basecode.ontology.AbstractOntologyTest;
import ubic.basecode.ontology.model.OntologyTerm;
import ubic.basecode.ontology.providers.GenericOntologyService;
+import ubic.basecode.ontology.search.OntologySearchResult;
import java.io.File;
import java.io.InputStream;
@@ -62,7 +63,7 @@ public void testCacheOntologyToDisk() throws Exception {
assertFalse( OntologyLoader.getTmpDiskCachePath( name ).exists() );
assertFalse( OntologyLoader.getOldDiskCachePath( name ).exists() );
- Collection r = s.findTerm( "Mouse" );
+ Collection> r = s.findTerm( "Mouse", 500 );
assertFalse( r.isEmpty() );
// Recreate OntologyService using this cache file
@@ -73,7 +74,7 @@ public void testCacheOntologyToDisk() throws Exception {
assertFalse( OntologyLoader.getTmpDiskCachePath( name ).exists() );
assertFalse( OntologyLoader.getOldDiskCachePath( name ).exists() );
- r = s.findTerm( "Mouse" );
+ r = s.findTerm( "Mouse", 500 );
assertFalse( r.isEmpty() );
// Recreate OntologyService with bad URL and no cache
diff --git a/test/ubic/basecode/ontology/jena/OntologySearchTest.java b/test/ubic/basecode/ontology/jena/OntologySearchTest.java
index 20bca5da..ed0d0631 100644
--- a/test/ubic/basecode/ontology/jena/OntologySearchTest.java
+++ b/test/ubic/basecode/ontology/jena/OntologySearchTest.java
@@ -16,20 +16,21 @@
import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.shared.JenaException;
import com.hp.hpl.jena.vocabulary.OWL2;
+import com.hp.hpl.jena.vocabulary.RDFS;
+import org.assertj.core.api.Assertions;
import org.junit.Test;
import ubic.basecode.ontology.AbstractOntologyTest;
import java.io.InputStream;
import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
import java.util.Set;
import java.util.zip.GZIPInputStream;
import static java.util.Objects.requireNonNull;
import static org.junit.Assert.*;
-import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.Mockito.*;
/**
* Most of these tests were moved over from Gemma.
@@ -43,17 +44,45 @@ public final void testIndexing() throws Exception {
InputStream is = new GZIPInputStream( requireNonNull( this.getClass().getResourceAsStream( "/data/mged.owl.gz" ) ) );
OntModel model = OntologyLoader.loadMemoryModel( is, "owl-test", false );
- SearchIndex index = OntologyIndexer.indexOntology( "MGEDTEST", model, true );
+ HashSet indexableProperties = new HashSet<>( OntologyIndexer.DEFAULT_INDEXABLE_PROPERTIES );
+ indexableProperties.add( new OntologyIndexer.IndexableProperty( RDFS.comment, true ) );
+ SearchIndex index = OntologyIndexer.indexOntology( "MGEDTEST", model, indexableProperties, Collections.emptySet(), true );
- Collection> name = OntologySearch.matchClasses( model, index, "Bedding" ).toSet();
+ Collection name = index.searchClasses( model, "Bedding", 500 ).toSet();
- assertEquals( 2, name.size() );
+ assertEquals( 1, name.size() );
index.close();
- index = OntologyIndexer.indexOntology( "MGEDTEST", model, true );
- name = OntologySearch.matchClasses( model, index, "Bedding" ).toSet();
+ index = OntologyIndexer.indexOntology( "MGEDTEST", model, indexableProperties, Collections.emptySet(), true );
+ name = index.searchClasses( model, "Bedding", 500 ).toSet();
+
+ assertEquals( 1, name.size() );
+ index.close();
+ }
+
+ @Test
+ public void testStemming() throws Exception {
+ InputStream is = new GZIPInputStream( requireNonNull( this.getClass().getResourceAsStream( "/data/mged.owl.gz" ) ) );
+ OntModel model = OntologyLoader.loadMemoryModel( is, "owl-test", false );
+ HashSet indexableProperties = new HashSet<>( OntologyIndexer.DEFAULT_INDEXABLE_PROPERTIES );
+ indexableProperties.add( new OntologyIndexer.IndexableProperty( RDFS.comment, true ) );
+ SearchIndex index = OntologyIndexer.indexOntology( "MGEDTEST", model, indexableProperties, Collections.emptySet(), true );
+
+ // bedding is stemmed to bed
+ Set results = index.searchClasses( model, "bed", 500 ).toSet();
+ Assertions.assertThat( results ).extracting( sr -> sr.result.as( OntClass.class ).getURI() )
+ .containsExactly( "http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Bedding" );
+
+ // plural query
+ results = index.searchClasses( model, "beddings", 500 ).toSet();
+ Assertions.assertThat( results ).extracting( sr -> sr.result.as( OntClass.class ).getURI() )
+ .containsExactly( "http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Bedding" );
+
+ // plural query
+ results = index.searchClasses( model, "beds", 500 ).toSet();
+ Assertions.assertThat( results ).extracting( sr -> sr.result.as( OntClass.class ).getURI() )
+ .containsExactly( "http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Bedding" );
- assertEquals( 2, name.size() );
index.close();
}
@@ -69,22 +98,24 @@ public final void testOmitBadPredicates() throws Exception {
model = OntologyLoader.loadMemoryModel( is, "NIFTEST" );
}
- SearchIndex index = OntologyIndexer.indexOntology( "NIFTEST", model, true );
+ HashSet indexableProperties = new HashSet<>( OntologyIndexer.DEFAULT_INDEXABLE_PROPERTIES );
+ indexableProperties.add( new OntologyIndexer.IndexableProperty( RDFS.comment, true ) );
+ SearchIndex index = OntologyIndexer.indexOntology( "NIFTEST", model, indexableProperties, Collections.emptySet(), true );
- Collection> name = OntologySearch.matchClasses( model, index, "Organ" ).toSet();
+ Collection name = index.searchClasses( model, "Organ", 500 ).toSet();
// for ( OntClass ontologyTerm : name ) {
// log.debug( ontologyTerm.toString() );
// }
// should get : Organ, Human Tissue and Organ Resource for Research, United Network for Organ Sharing
assertEquals( 3, name.size() );
- name = OntologySearch.matchClasses( model, index, "Anatomical entity" ).toSet();
+ name = index.searchClasses( model, "Anatomical entity", 500 ).toSet();
// for ( OntClass ontologyTerm : name ) {
// log.debug( ontologyTerm.toString() );
// }
assertEquals( 1, name.size() );
- name = OntologySearch.matchClasses( model, index, "liver" ).toSet(); // this is an "example" that we want to avoid
+ name = index.searchClasses( model, "liver", 500 ).toSet(); // this is an "example" that we want to avoid
// leading to "Organ".
// for ( OntClass ontologyTerm : name ) {
@@ -106,16 +137,16 @@ public final void testOmitBadPredicates2() throws Exception {
model = OntologyLoader.loadMemoryModel( is, "EFTEST" );
}
- SearchIndex index = OntologyIndexer.indexOntology( "EFTEST", model, true );
+ SearchIndex index = OntologyIndexer.indexOntology( "EFTEST", model, Collections.emptySet(), true );
// positive control
- Collection> searchResults = OntologySearch.matchClasses( model, index, "monocyte" ).toSet();
+ Collection searchResults = index.searchClasses( model, "monocyte", 500 ).toSet();
assertFalse( "Should have found something for 'monocyte'", searchResults.isEmpty() );
assertEquals( 1, searchResults.size() );
// this is a "definition" that we want to avoid leading to "Monocyte".
- searchResults = OntologySearch.matchClasses( model, index, "liver" ).toSet();
- for ( OntologySearch.SearchResult ontologyTerm : searchResults ) {
+ searchResults = index.searchClasses( model, "liver", 500 ).toSet();
+ for ( SearchIndex.JenaSearchResult ontologyTerm : searchResults ) {
fail( "Should not have found " + ontologyTerm.toString() );
}
@@ -130,15 +161,15 @@ public final void testOmitDefinitions() throws Exception {
model = OntologyLoader.loadMemoryModel( is, "DO_TEST" );
}
- SearchIndex index = OntologyIndexer.indexOntology( "DO_TEST", model, true );
+ SearchIndex index = OntologyIndexer.indexOntology( "DO_TEST", model, Collections.emptySet(), true );
// positive control
- Set> searchResults = OntologySearch.matchClasses( model, index, "acute leukemia" ).toSet();
+ Set searchResults = index.searchClasses( model, "acute leukemia", 500 ).toSet();
assertFalse( "Should have found something for 'acute leukemia'", searchResults.isEmpty() );
// this is a "definition" that we want to avoid leading to "acute leukemia".
- searchResults = OntologySearch.matchClasses( model, index, "liver" ).toSet();
- for ( OntologySearch.SearchResult ontologyTerm : searchResults ) {
+ searchResults = index.searchClasses( model, "liver", 500 ).toSet();
+ for ( SearchIndex.JenaSearchResult ontologyTerm : searchResults ) {
fail( "Should not have found " + ontologyTerm.toString() );
}
@@ -153,33 +184,36 @@ public final void testOmitDefinitions2() throws Exception {
model = OntologyLoader.loadMemoryModel( is, "NIFORG_TEST", false );
}
- SearchIndex index = OntologyIndexer.indexOntology( "NIFORG_TEST", model, true );
+ HashSet indexableProperties = new HashSet<>( OntologyIndexer.DEFAULT_INDEXABLE_PROPERTIES );
+ indexableProperties.add( new OntologyIndexer.IndexableProperty( RDFS.comment, true ) );
+ SearchIndex index = OntologyIndexer.indexOntology( "NIFORG_TEST", model, indexableProperties, Collections.emptySet(), true );
// positive control
- Collection> searchResults = OntologySearch.matchClasses( model, index, "Mammal" ).toSet();
+ Collection searchResults = index.searchClasses( model, "Mammal", 500 ).toSet();
assertFalse( "Should have found something for 'Mammal'", searchResults.isEmpty() );
// this is a "definition" that we want to avoid leading to "acute leukemia".
- searchResults = OntologySearch.matchClasses( model, index, "skin" ).toSet();
- for ( OntologySearch.SearchResult ontologyTerm : searchResults ) {
+ searchResults = index.searchClasses( model, "skin", 500 ).toSet();
+ for ( SearchIndex.JenaSearchResult ontologyTerm : searchResults ) {
fail( "Should not have found " + ontologyTerm.toString() + " for 'skin'" );
}
- searchResults = OntologySearch.matchClasses( model, index, "approximate" ).toSet();
- for ( OntologySearch.SearchResult ontologyTerm : searchResults ) {
+ searchResults = index.searchClasses( model, "approximate", 500 ).toSet();
+ for ( SearchIndex.JenaSearchResult ontologyTerm : searchResults ) {
fail( "Should not have found " + ontologyTerm.toString() + " for 'approximate'" );
}
- searchResults = OntologySearch.matchClasses( model, index, "Bug" ).toSet();
- for ( OntologySearch.SearchResult ontologyTerm : searchResults ) {
+ searchResults = index.searchClasses( model, "Bug", 500 ).toSet();
+ for ( SearchIndex.JenaSearchResult ontologyTerm : searchResults ) {
fail( "Should not have found " + ontologyTerm.toString() + " for 'Bug'" );
}
- searchResults = OntologySearch.matchClasses( model, index, "birnlex_2" )
+ searchResults = index.searchClasses( model, "birnlex_2", 500 )
.toSet();
- assertEquals( 1, searchResults.size() );
- assertTrue( searchResults.iterator().next().result.hasLiteral( OWL2.deprecated, true ) );
-
+ Assertions.assertThat( searchResults ).hasSize( 1 ).extracting( sr -> sr.result )
+ .satisfiesOnlyOnce( r -> {
+ assertTrue( r.as( OntClass.class ).hasLiteral( OWL2.deprecated, true ) );
+ } );
index.close();
}
@@ -191,15 +225,15 @@ public final void testOmitDefinitions3() throws Exception {
model = OntologyLoader.loadMemoryModel( is, "OBI_TEST" );
}
- SearchIndex index = OntologyIndexer.indexOntology( "OBI_TEST", model, true );
+ SearchIndex index = OntologyIndexer.indexOntology( "OBI_TEST", model, Collections.emptySet(), true );
// positive control
- Set> searchResults = OntologySearch.matchClasses( model, index, "irradiation" ).toSet();
+ Set searchResults = index.searchClasses( model, "irradiation", 500 ).toSet();
assertFalse( "Should have found something for 'irradiation'", searchResults.isEmpty() );
// this is a "definition" that we want to avoid leading to "acute leukemia".
- searchResults = OntologySearch.matchClasses( model, index, "skin" ).toSet();
- for ( OntologySearch.SearchResult ontologyTerm : searchResults ) {
+ searchResults = index.searchClasses( model, "skin", 500 ).toSet();
+ for ( SearchIndex.JenaSearchResult ontologyTerm : searchResults ) {
fail( "Should not have found " + ontologyTerm.toString() + " for 'skin'" );
}
@@ -213,15 +247,15 @@ public final void testOmitDefinitions4() throws Exception {
OntModel model = OntologyLoader.loadMemoryModel( is, "NIFAN_TEST2", false );
is.close();
- SearchIndex index = OntologyIndexer.indexOntology( "NIFAN_TEST2", model, true );
+ SearchIndex index = OntologyIndexer.indexOntology( "NIFAN_TEST2", model, Collections.emptySet(), true );
// positive control
- Collection> searchResults = OntologySearch.matchClasses( model, index, "eye" ).toSet();
+ Collection searchResults = index.searchClasses( model, "eye", 500 ).toSet();
assertFalse( "Should have found something for 'eye'", searchResults.isEmpty() );
// this is a "definition" that we want to avoid leading to "brain"
- searchResults = OntologySearch.matchClasses( model, index, "muscle" ).toSet();
- for ( OntologySearch.SearchResult ontologyTerm : searchResults ) {
+ searchResults = index.searchClasses( model, "muscle", 500 ).toSet();
+ for ( SearchIndex.JenaSearchResult ontologyTerm : searchResults ) {
fail( "Should not have found " + ontologyTerm.toString() + " for 'muscle'" );
}
@@ -234,60 +268,30 @@ public final void testPersistence() throws Exception {
InputStream is = new GZIPInputStream( requireNonNull( this.getClass().getResourceAsStream( "/data/mged.owl.gz" ) ) );
OntModel model = OntologyLoader.loadMemoryModel( is, "owl-test", false );
- SearchIndex index = OntologyIndexer.indexOntology( "MGEDTEST", model, false );
+ HashSet indexableProperties = new HashSet<>( OntologyIndexer.DEFAULT_INDEXABLE_PROPERTIES );
+ indexableProperties.add( new OntologyIndexer.IndexableProperty( RDFS.comment, true ) );
+
+ SearchIndex index = OntologyIndexer.indexOntology( "MGEDTEST", model, indexableProperties, Collections.emptySet(), false );
index.close();
// now load it off disk
- index = OntologyIndexer.getSubjectIndex( "MGEDTEST" );
+ index = OntologyIndexer.getSubjectIndex( "MGEDTEST", indexableProperties, Collections.emptySet() );
assertNotNull( index );
- Collection> name = OntologySearch.matchClasses( model, index, "bedding" ).toSet();
- assertEquals( 2, name.size() );
+ Collection name = index.searchClasses( model, "bedding", 500 ).toSet();
+ assertEquals( 1, name.size() );
// test wildcard. Works with stemmed term, wild card doesn't do anything
- name = OntologySearch.matchClasses( model, index, "bed*" ).toSet();
+ name = index.searchClasses( model, "bed*", 500 ).toSet();
assertEquals( 2, name.size() );
// stemmed term.
- name = OntologySearch.matchClasses( model, index, "bed" ).toSet();
- assertEquals( 2, name.size() );
+ name = index.searchClasses( model, "bed", 500 ).toSet();
+ assertEquals( 1, name.size() );
- name = OntologySearch.matchClasses( model, index, "beddin*" ).toSet();
+ name = index.searchClasses( model, "beddin*", 500 ).toSet();
assertEquals( 2, name.size() );
index.close();
}
-
- @Test
- public final void matchClasses_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException() {
- OntModel model = mock( OntModel.class );
- SearchIndex index = mock( SearchIndex.class );
- when( index.search( any() ) ).thenThrow( new JenaException( "Some random exception raised by Jena." ) );
- OntologySearchJenaException e = assertThrows( OntologySearchJenaException.class, () -> OntologySearch.matchClasses( model, index, "test" ) );
- assertEquals( "test", e.getQuery() );
- assertEquals( "Some random exception raised by Jena.", e.getCause().getMessage() );
- verify( index ).search( "test" );
- }
-
- @Test
- public final void matchIndividuals_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException() {
- OntModel model = mock( OntModel.class );
- SearchIndex index = mock( SearchIndex.class );
- when( index.search( any() ) ).thenThrow( new JenaException( "Some random exception raised by Jena." ) );
- OntologySearchJenaException e = assertThrows( OntologySearchJenaException.class, () -> OntologySearch.matchIndividuals( model, index, "test" ) );
- assertEquals( "test", e.getQuery() );
- assertEquals( "Some random exception raised by Jena.", e.getCause().getMessage() );
- verify( index ).search( "test" );
- }
-
- @Test
- public final void matchResources_whenIndexRaisesJenaException_thenWrapItWithOntologyJenaSearchException() {
- OntModel model = mock( OntModel.class );
- SearchIndex index = mock( SearchIndex.class );
- when( index.search( any() ) ).thenThrow( new JenaException( "Some random exception raised by Jena." ) );
- OntologySearchJenaException e = assertThrows( OntologySearchJenaException.class, () -> OntologySearch.matchIndividuals( model, index, "test" ) );
- assertEquals( "test", e.getQuery() );
- assertEquals( "Some random exception raised by Jena.", e.getCause().getMessage() );
- verify( index ).search( "test" );
- }
}
diff --git a/test/ubic/basecode/ontology/jena/UberonOntologySearchTest.java b/test/ubic/basecode/ontology/jena/UberonOntologySearchTest.java
index f0c41fc5..7c325c5d 100644
--- a/test/ubic/basecode/ontology/jena/UberonOntologySearchTest.java
+++ b/test/ubic/basecode/ontology/jena/UberonOntologySearchTest.java
@@ -3,12 +3,14 @@
import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
+import com.hp.hpl.jena.vocabulary.RDFS;
import org.junit.BeforeClass;
import org.junit.Test;
import ubic.basecode.ontology.search.OntologySearchException;
import java.io.IOException;
import java.io.InputStream;
+import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -26,7 +28,9 @@ public class UberonOntologySearchTest {
public static void setUpUberon() throws IOException {
try ( InputStream is = new GZIPInputStream( requireNonNull( OntologySearchTest.class.getResourceAsStream( "/data/uberon.owl.gz" ) ) ) ) {
uberon = OntologyLoader.loadMemoryModel( is, "UBERON_TEST2", true, OntModelSpec.OWL_MEM );
- uberonIndex = OntologyIndexer.indexOntology( "UBERON_TEST2", uberon, false );
+ HashSet indexableProperties = new HashSet<>( OntologyIndexer.DEFAULT_INDEXABLE_PROPERTIES );
+ indexableProperties.add( new OntologyIndexer.IndexableProperty( RDFS.comment, true ) );
+ uberonIndex = OntologyIndexer.indexOntology( "UBERON_TEST2", uberon, indexableProperties, Collections.emptySet(), true );
}
}
@@ -34,7 +38,7 @@ public static void setUpUberon() throws IOException {
public void testOmitDefinition() throws OntologySearchException {
OntClass brain = uberon.getOntClass( "http://purl.obolibrary.org/obo/UBERON_0000955" );
assertNotNull( brain );
- Set> searchResults = OntologySearch.matchClasses( uberon, uberonIndex, "brain" ).toSet();
+ Set searchResults = uberonIndex.searchClasses( uberon, "brain", 500 ).toSet();
assertEquals( 128, searchResults.size() );
}
@@ -42,9 +46,8 @@ public void testOmitDefinition() throws OntologySearchException {
public void testScore() throws OntologySearchException {
OntClass brain = uberon.getOntClass( "http://purl.obolibrary.org/obo/UBERON_0000955" );
assertNotNull( brain );
- List> searchResults = OntologySearch.matchClasses( uberon, uberonIndex, "brain" ).toList();
- assertEquals( 446, searchResults.size() );
- assertEquals( 3.33, searchResults.get( 0 ).score, 0.01 );
- assertEquals( 128, new HashSet<>( searchResults ).size() );
+ List searchResults = uberonIndex.searchClasses( uberon, "brain", 500 ).toList();
+ assertEquals( 128, searchResults.size() );
+ assertEquals( 3.85, searchResults.get( 0 ).score, 0.01 );
}
}
diff --git a/test/ubic/basecode/ontology/providers/GenericOntologyServiceTest.java b/test/ubic/basecode/ontology/providers/GenericOntologyServiceTest.java
index 09f25e7d..a74cb90a 100644
--- a/test/ubic/basecode/ontology/providers/GenericOntologyServiceTest.java
+++ b/test/ubic/basecode/ontology/providers/GenericOntologyServiceTest.java
@@ -19,9 +19,11 @@
package ubic.basecode.ontology.providers;
+import org.assertj.core.api.Assertions;
import org.junit.Test;
import ubic.basecode.ontology.AbstractOntologyTest;
import ubic.basecode.ontology.model.OntologyTerm;
+import ubic.basecode.ontology.search.OntologySearchResult;
import ubic.basecode.util.Configuration;
import java.net.URL;
@@ -44,7 +46,7 @@ public void testGenericOntologyServiceMem() throws Exception {
s1.initialize( true, false );
GenericOntologyService s = s1;
- Collection r = s.findTerm( "Mouse" );
+ Collection> r = s.findTerm( "Mouse", 500 );
assertFalse( r.isEmpty() );
}
@@ -79,10 +81,10 @@ public void testWithoutOntologyCacheDir() {
new GenericOntologyService( "foo", resource.toString(), false, false )
.initialize( true, true );
} );
- assertTrue( e.getMessage().matches( "No cache directory is set for foo \\[file:.+], cannot force indexing." ) );
+ Assertions.assertThat( e )
+ .hasMessageMatching( "No cache directory is set for foo.+, cannot force indexing\\." );
} finally {
- Configuration.setString( "ontology.cache.dir", prevCacheDir );
- Configuration.setString( "ontology.index.dir", prevIndexDir );
+ Configuration.reset();
}
}
}
diff --git a/test/ubic/basecode/ontology/providers/ObiServiceTest.java b/test/ubic/basecode/ontology/providers/ObiServiceTest.java
index 6dd8752d..b8aeb354 100644
--- a/test/ubic/basecode/ontology/providers/ObiServiceTest.java
+++ b/test/ubic/basecode/ontology/providers/ObiServiceTest.java
@@ -16,14 +16,10 @@
import org.junit.Test;
import ubic.basecode.ontology.AbstractOntologyTest;
-import ubic.basecode.ontology.model.OntologyIndividual;
import ubic.basecode.ontology.model.OntologyResource;
-import ubic.basecode.ontology.model.OntologyTerm;
+import ubic.basecode.ontology.search.OntologySearchResult;
-import java.util.Collection;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.assertj.core.api.Assertions.assertThat;
/**
* @author paul
@@ -35,16 +31,21 @@ public void testLoadAndSearch() throws Exception {
ObiService m = new ObiService();
m.setInferenceMode( OntologyService.InferenceMode.NONE );
m.initialize( true, false );
-
- assertTrue( m.isOntologyLoaded() );
-
- Collection hits = m.findTerm( "batch" );
- assertFalse( hits.isEmpty() );
-
- Collection ihits = m.findIndividuals( "batch" );
- assertFalse( ihits.isEmpty() );
-
- Collection rhits = m.findResources( "batch" );
- assertFalse( rhits.isEmpty() );
+ assertThat( m.isOntologyLoaded() ).isTrue();
+
+ assertThat( m.findTerm( "batch", 500 ) )
+ .extracting( OntologySearchResult::getResult )
+ .extracting( OntologyResource::getUri )
+ .contains( "http://purl.obolibrary.org/obo/IAO_0000132" );
+
+ assertThat( m.findIndividuals( "failed exploratory term", 500 ) )
+ .extracting( OntologySearchResult::getResult )
+ .extracting( OntologyResource::getUri )
+ .contains( "http://purl.obolibrary.org/obo/IAO_0000103" );
+
+ assertThat( m.findResources( "batch", 500 ) )
+ .extracting( OntologySearchResult::getResult )
+ .extracting( OntologyResource::getUri )
+ .contains( "http://purl.obolibrary.org/obo/IAO_0000132" );
}
}
diff --git a/test/ubic/basecode/ontology/providers/UberonOntologyServiceTest.java b/test/ubic/basecode/ontology/providers/UberonOntologyServiceTest.java
index 9ae9754e..ad4d3810 100644
--- a/test/ubic/basecode/ontology/providers/UberonOntologyServiceTest.java
+++ b/test/ubic/basecode/ontology/providers/UberonOntologyServiceTest.java
@@ -7,11 +7,13 @@
import ubic.basecode.ontology.OntologyTermTest;
import ubic.basecode.ontology.model.OntologyTerm;
import ubic.basecode.ontology.search.OntologySearchException;
+import ubic.basecode.ontology.search.OntologySearchResult;
import java.io.IOException;
import java.io.InputStream;
import java.util.Arrays;
import java.util.Collection;
+import java.util.stream.Collectors;
import java.util.zip.GZIPInputStream;
import static java.util.Objects.requireNonNull;
@@ -55,7 +57,7 @@ public void testGetParentsFromMultipleTerms() {
OntologyTerm brain = uberon.getTerm( "http://purl.obolibrary.org/obo/UBERON_0000955" );
OntologyTerm liver = uberon.getTerm( "http://purl.obolibrary.org/obo/UBERON_0002107" );
Collection children = uberon.getParents( Arrays.asList( brain, liver ), false, true );
- assertEquals( 30, children.size() );
+ assertEquals( 41, children.size() );
assertFalse( children.contains( uberon.getTerm( OWL2.Nothing.getURI() ) ) );
}
@@ -64,7 +66,7 @@ public void testGetParentsHasPart() {
OntologyTerm t = uberon.getTerm( "http://purl.obolibrary.org/obo/UBERON_0000955" );
assertNotNull( t );
Collection parents = t.getParents( true );
- assertEquals( 3, parents.size() );
+ assertEquals( 4, parents.size() );
// does not contain itself
assertFalse( parents.contains( t ) );
// via subclass
@@ -79,9 +81,9 @@ public void testGetParentsHasPart() {
public void testGetChildrenHasPart() {
OntologyTerm t = uberon.getTerm( "http://purl.obolibrary.org/obo/UBERON_0000955" );
assertNotNull( t );
- assertEquals( 76, t.getChildren( true ).size() );
+ assertEquals( 81, t.getChildren( true ).size() );
Collection children = t.getChildren( false );
- assertEquals( 1496, children.size() );
+ assertEquals( 1995, children.size() );
// via subclass of, insect adult brain
assertTrue( children.contains( uberon.getTerm( "http://purl.obolibrary.org/obo/UBERON_6003624" ) ) );
// via part of, nucleus of brain
@@ -95,22 +97,22 @@ public void testGetChildrenFromMultipleTerms() {
OntologyTerm brain = uberon.getTerm( "http://purl.obolibrary.org/obo/UBERON_0000955" );
OntologyTerm liver = uberon.getTerm( "http://purl.obolibrary.org/obo/UBERON_0002107" );
Collection children = uberon.getChildren( Arrays.asList( brain, liver ), false, true );
- assertEquals( 1562, children.size() );
+ assertEquals( 2077, children.size() );
}
@Test
public void testGetChildrenFromMultipleTermsWithSearch() throws OntologySearchException {
- Collection terms = uberon.findTerm( "brain" );
- Collection matches = uberon.getChildren( terms, false, true );
- assertEquals( 1870, matches.size() );
+ Collection> terms = uberon.findTerm( "brain", 500 );
+ Collection matches = uberon.getChildren( terms.stream().map( OntologySearchResult::getResult ).collect( Collectors.toSet() ), false, true );
+ assertEquals( 2684, matches.size() );
}
@Test
public void testFindTerm() throws OntologySearchException {
- assertEquals( 123, uberon.findTerm( "brain" ).size() );
- assertEquals( 128, uberon.findTerm( "brain", true ).size() );
- OntologyTerm firstResult = uberon.findTerm( "brain" ).iterator().next();
- assertNotNull( firstResult.getScore() );
- assertEquals( 2.8577, firstResult.getScore(), 0.0001 );
+ assertEquals( 98, uberon.findTerm( "brain", 500 ).size() );
+ assertEquals( 103, uberon.findTerm( "brain", 500, true ).size() );
+ OntologySearchResult firstResult = uberon.findTerm( "brain", 500 ).iterator().next();
+ assertNotNull( firstResult );
+ assertEquals( 1.5367, firstResult.getScore(), 0.0001 );
}
}