diff --git a/aspiredb/pom.xml b/aspiredb/pom.xml index b6339d10..fbc175bf 100644 --- a/aspiredb/pom.xml +++ b/aspiredb/pom.xml @@ -12,7 +12,7 @@ ubc.pavlab pavlab-starter-parent - 1.0 + 1.1.8 @@ -21,7 +21,7 @@ 1.8 3.2.18.RELEASE 3.2.10.RELEASE - 0.0.7 + 0.0.8 @@ -209,10 +209,8 @@ - javassist + org.javassist javassist - 3.12.1.GA - runtime org.hibernate diff --git a/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/ontology/OntologyService.java b/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/ontology/OntologyService.java index 6b070b0d..5424bf59 100644 --- a/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/ontology/OntologyService.java +++ b/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/ontology/OntologyService.java @@ -24,6 +24,7 @@ import ubic.basecode.ontology.model.OntologyTerm; import ubic.basecode.ontology.providers.DiseaseOntologyService; import ubic.basecode.ontology.providers.HumanPhenotypeOntologyService; +import ubic.basecode.ontology.search.OntologySearchException; /** * @author paul @@ -35,7 +36,7 @@ public interface OntologyService extends InitializingBean { * @param givenSearch * @return */ - public Collection findIndividuals( String givenSearch ); + public Collection findIndividuals( String givenSearch ) throws OntologySearchException; /** * Given a search string will look through the loaded ontologies for terms that match the search term. this a lucene @@ -44,7 +45,7 @@ public interface OntologyService extends InitializingBean { * @param search * @return returns a collection of ontologyTerm's */ - public Collection findTerms( String search ); + public Collection findTerms( String search ) throws OntologySearchException; /** * @return the diseaseOntologyService diff --git a/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/ontology/OntologyServiceImpl.java b/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/ontology/OntologyServiceImpl.java index 6073e806..f09fe508 100644 --- a/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/ontology/OntologyServiceImpl.java +++ b/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/ontology/OntologyServiceImpl.java @@ -28,6 +28,7 @@ import ubic.basecode.ontology.providers.DiseaseOntologyService; import ubic.basecode.ontology.providers.HumanPhenotypeOntologyService; import ubic.basecode.ontology.search.OntologySearch; +import ubic.basecode.ontology.search.OntologySearchException; /** * Has a static method for finding out which ontologies are loaded into the system and a general purpose find method @@ -64,7 +65,7 @@ public void afterPropertiesSet() { } @Override - public Collection findIndividuals( String givenSearch ) { + public Collection findIndividuals( String givenSearch ) throws OntologySearchException { String query = OntologySearch.stripInvalidCharacters( givenSearch ); Collection results = new HashSet(); @@ -80,7 +81,7 @@ public Collection findIndividuals( String givenSearch ) { } @Override - public Collection findTerms( String search ) { + public Collection findTerms( String search ) throws OntologySearchException { String query = OntologySearch.stripInvalidCharacters( search ); diff --git a/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/service/QueryService.java b/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/service/QueryService.java index 9b661d0e..73360eb0 100644 --- a/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/service/QueryService.java +++ b/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/service/QueryService.java @@ -38,6 +38,7 @@ import ubc.pavlab.aspiredb.shared.suggestions.PhenotypeSuggestion; import com.sencha.gxt.data.shared.loader.PagingLoadResult; +import ubic.basecode.ontology.search.OntologySearchException; /** * Methods for various query operations such as querying a list of subjects and variants given a list of filters, @@ -53,7 +54,7 @@ public BoundedList querySubjects( Set public BoundedList queryVariants( Set filters ) throws NotLoggedInException, ExternalDependencyException; - public PagingLoadResult getOntologyTermSuggestions( String query ); + public PagingLoadResult getOntologyTermSuggestions( String query ) throws OntologySearchException; public List getValuesForOntologyTerm( String ontologyTermUri ); diff --git a/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/service/QueryServiceImpl.java b/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/service/QueryServiceImpl.java index 28a41987..105bafd6 100644 --- a/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/service/QueryServiceImpl.java +++ b/aspiredb/src/main/java/ubc/pavlab/aspiredb/server/service/QueryServiceImpl.java @@ -77,6 +77,7 @@ import ubc.pavlab.aspiredb.shared.suggestions.PhenotypeSuggestion; import ubic.basecode.ontology.model.OntologyTerm; import ubic.basecode.ontology.providers.HumanPhenotypeOntologyService; +import ubic.basecode.ontology.search.OntologySearchException; /** * Methods for various query operations such as querying a list of subjects and variants given a list of filters, @@ -151,7 +152,7 @@ public PagingLoadResult getNeurocartaPhenotypeSu } @Override - public PagingLoadResult getOntologyTermSuggestions( String query ) { + public PagingLoadResult getOntologyTermSuggestions( String query ) throws OntologySearchException { HumanPhenotypeOntologyService HPOService = ontologyService.getHumanPhenotypeOntologyService(); // if ( !HPOService.isOntologyLoaded() ) { // HPOService.startInitializationThread( true ); diff --git a/aspiredb/src/test/java/ubc/pavlab/aspiredb/server/controller/SignupControllerTest.java b/aspiredb/src/test/java/ubc/pavlab/aspiredb/server/controller/SignupControllerTest.java index 9007a287..f45e496f 100644 --- a/aspiredb/src/test/java/ubc/pavlab/aspiredb/server/controller/SignupControllerTest.java +++ b/aspiredb/src/test/java/ubc/pavlab/aspiredb/server/controller/SignupControllerTest.java @@ -15,7 +15,7 @@ package ubc.pavlab.aspiredb.server.controller; import static org.junit.Assert.fail; -import static org.mockito.Matchers.any; +import static org.mockito.Mockito.any; import static org.mockito.Mockito.when; import java.util.ArrayList;