Update pavlab-starter-parent to 1.1.8

aspiredb/pom.xml

@@ -12,7 +12,7 @@
     <parent>
         <groupId>ubc.pavlab</groupId>
         <artifactId>pavlab-starter-parent</artifactId>
-        <version>1.0</version>
+        <version>1.1.8</version>
     </parent>
 
     <properties>
@@ -21,7 +21,7 @@
         <maven.compiler.target>1.8</maven.compiler.target>
         <spring.version>3.2.18.RELEASE</spring.version>
         <spring.security.version>3.2.10.RELEASE</spring.security.version>
-        <gsec.version>0.0.7</gsec.version>
+        <gsec.version>0.0.8</gsec.version>
     </properties>
 
     <repositories>
@@ -209,10 +209,8 @@
         </dependency>
         <dependency>
             <!-- required by hibernate, explicitly import so we get it at runtime. -->
-            <groupId>javassist</groupId>
+            <groupId>org.javassist</groupId>
             <artifactId>javassist</artifactId>
-            <version>3.12.1.GA</version>
-            <scope>runtime</scope>
         </dependency>
         <dependency>
             <groupId>org.hibernate</groupId>

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<OntologyIndividual> findIndividuals( String givenSearch );
+    public Collection<OntologyIndividual> 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<OntologyTerm> findTerms( String search );
+    public Collection<OntologyTerm> findTerms( String search ) throws OntologySearchException;
 
     /**
      * @return the diseaseOntologyService

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<OntologyIndividual> findIndividuals( String givenSearch ) {
+    public Collection<OntologyIndividual> findIndividuals( String givenSearch ) throws OntologySearchException {
 
         String query = OntologySearch.stripInvalidCharacters( givenSearch );
         Collection<OntologyIndividual> results = new HashSet<OntologyIndividual>();
@@ -80,7 +81,7 @@ public Collection<OntologyIndividual> findIndividuals( String givenSearch ) {
     }
 
     @Override
-    public Collection<OntologyTerm> findTerms( String search ) {
+    public Collection<OntologyTerm> findTerms( String search ) throws OntologySearchException {
 
         String query = OntologySearch.stripInvalidCharacters( search );
 

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<SubjectValueObject> querySubjects( Set<AspireDbFilterConfig>
     public BoundedList<VariantValueObject> queryVariants( Set<AspireDbFilterConfig> filters )
             throws NotLoggedInException, ExternalDependencyException;
 
-    public PagingLoadResult<OntologyTermValueObject> getOntologyTermSuggestions( String query );
+    public PagingLoadResult<OntologyTermValueObject> getOntologyTermSuggestions( String query ) throws OntologySearchException;
 
     public List<String> getValuesForOntologyTerm( String ontologyTermUri );
 

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<NeurocartaPhenotypeValueObject> getNeurocartaPhenotypeSu
     }
 
     @Override
-    public PagingLoadResult<OntologyTermValueObject> getOntologyTermSuggestions( String query ) {
+    public PagingLoadResult<OntologyTermValueObject> getOntologyTermSuggestions( String query ) throws OntologySearchException {
         HumanPhenotypeOntologyService HPOService = ontologyService.getHumanPhenotypeOntologyService();
         // if ( !HPOService.isOntologyLoaded() ) {
         // HPOService.startInitializationThread( true );

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;