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;