Merge branch 'hotfix-1.5.1'

pom.xml

@@ -5,7 +5,7 @@
 
     <groupId>ubc.pavlab</groupId>
     <artifactId>rdp</artifactId>
-    <version>1.5.0</version>
+    <version>1.5.1</version>
 
     <description>
         Registry for model organism researchers, developed for the Canadian Rare Disease Models &amp; Mechanisms Network.
@@ -28,7 +28,7 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.6.10</version>
+        <version>2.6.12</version>
     </parent>
 
     <dependencies>
@@ -108,7 +108,7 @@
         <dependency>
             <groupId>org.springdoc</groupId>
             <artifactId>springdoc-openapi-webmvc-core</artifactId>
-            <version>1.6.9</version>
+            <version>1.6.11</version>
         </dependency>
 
         <!-- Database Migration -->

src/main/java/ubc/pavlab/rdp/controllers/AbstractSearchController.java

@@ -291,7 +291,7 @@ protected Map<URI, List<OntologyAvailability>> getOntologyAvailabilityByApiUri(
 
         Map<URI, List<OntologyAvailability>> availability = new HashMap<>();
         for ( URI remoteHost : remoteResourceService.getApiUris() ) {
-            List<OntologyAvailability> availabilities = new ArrayList<>();
+            List<OntologyAvailability> availabilities = new ArrayList<>( termsByOntology.size() );
             // lookup origin and origin URL in all terms from all ontologies
             // when an ontology is not present, there are no terms returned and thus no way to determine the origin, so
             // we increase our chance by of finding something useful this way

src/main/java/ubc/pavlab/rdp/controllers/AdminController.java

@@ -167,7 +167,7 @@ public Object updateRoles( @PathVariable User user, @RequestParam(required = fal
             }
         } catch ( RoleException e ) {
             redirectAttributes.addFlashAttribute( "message", e.getMessage() );
-            redirectAttributes.addFlashAttribute( "error", true );
+            redirectAttributes.addFlashAttribute( "error", Boolean.TRUE );
         }
         return "redirect:/admin/users/" + user.getId();
 
@@ -361,9 +361,9 @@ public Object deleteOntology( @PathVariable(required = false) Ontology ontology,
                 redirectAttributes.addFlashAttribute( "message", String.format( "The %s category has been deleted.", messageSource.getMessage( ontology.getResolvableTitle(), locale ) ) );
                 return "redirect:/admin/ontologies";
             } catch ( DataIntegrityViolationException e ) {
-                log.warn( String.format( "An administrator attempted to delete %s, but it failed: %s", ontology, e.getMessage() ) );
+                log.warn( String.format( "An administrator attempted to delete %s, but it failed: %s", ontology.toString().replaceAll( "[\r\n]", "" ), e.getMessage() ) );
                 modelAndView.setStatus( HttpStatus.BAD_REQUEST );
-                modelAndView.addObject( "error", true );
+                modelAndView.addObject( "error", Boolean.TRUE );
                 modelAndView.addObject( "message", String.format( "The %s category could not be deleted because it is being used. Instead, you should deactivate it.", messageSource.getMessage( ontology.getResolvableTitle(), locale ) ) );
             }
         }
@@ -592,9 +592,9 @@ public void validate( Object target, Errors errors ) {
                     .filter( row -> !row.isEmpty() )
                     .map( SimpleOntologyTermForm::getTermId )
                     .filter( termId -> !StringUtils.isEmpty( termId ) ) // empty or null term IDs are generated
-                    .collect( Collectors.groupingBy( t -> t, Collectors.counting() ) );
+                    .collect( Collectors.groupingBy( identity(), Collectors.counting() ) );
             if ( countsByTermId.values().stream().anyMatch( x -> x > 1 ) ) {
-                errors.rejectValue( "ontologyTerms", "AdminController.SimpleOntologyForm.ontologyTerms.nonUniqueTermIds", "termId must be unique" );
+                errors.rejectValue( "ontologyTerms", "AdminController.SimpleOntologyForm.ontologyTerms.nonUniqueTermIds" );
             }
 
             // validate non-empty rows
@@ -643,19 +643,19 @@ public Object updateOntology( @PathVariable(required = false) Ontology ontology,
             return new ModelAndView( "admin/ontology", HttpStatus.BAD_REQUEST )
                     .addAllObjects( defaultsForOntologyModelAndView( ontology ) )
                     .addObject( "message", "The provided ontology cannot be updated because it lacks an external URL." )
-                    .addObject( "error", true );
+                    .addObject( "error", Boolean.TRUE );
         } else {
             Resource urlResource = ontologyService.resolveOntologyUrl( ontology.getOntologyUrl() );
             try ( Reader reader = new InputStreamReader( urlResource.getInputStream() ) ) {
                 ontologyService.updateFromObo( ontology, reader );
                 int numActivated = ontologyService.propagateSubtreeActivation( ontology );
                 redirectAttributes.addFlashAttribute( "message", String.format( "Updated %s from %s. %d terms got activated via subtree propagation.", messageSource.getMessage( ontology.getResolvableTitle(), locale ), ontology.getOntologyUrl(), numActivated ) );
             } catch ( IOException | ParseException e ) {
-                log.warn( String.format( "Failed to update ontology %s from administrative section.", ontology ), e );
+                log.warn( String.format( "Failed to update ontology %s from administrative section.", ontology.toString().replaceAll( "[\r\n]", "" ) ), e );
                 return new ModelAndView( "admin/ontology", HttpStatus.BAD_REQUEST )
                         .addAllObjects( defaultsForOntologyModelAndView( ontology ) )
                         .addObject( "message", String.format( "Failed to update %s: %s", messageSource.getMessage( ontology.getResolvableTitle(), locale ), e.getMessage() ) )
-                        .addObject( "error", true );
+                        .addObject( "error", Boolean.TRUE );
             }
         }
         return "redirect:/admin/ontologies/" + ontology.getId();
@@ -673,14 +673,12 @@ public Object importOntology( @Valid ImportOntologyForm importOntologyForm, Bind
             ontologyService.update( ontology );
             return "redirect:/admin/ontologies/" + ontology.getId();
         } catch ( OntologyNameAlreadyUsedException e ) {
-            bindingResult.reject( "AdminController.ImportOntologyForm.ontologyWithSameNameAlreadyUsed", new String[]{ e.getOntologyName() },
-                    String.format( "An ontology with the same name '%s' is already used.", e.getOntologyName() ) );
+            bindingResult.reject( "AdminController.ImportOntologyForm.ontologyWithSameNameAlreadyUsed", new String[]{ e.getOntologyName() }, null );
             return new ModelAndView( "admin/ontologies", HttpStatus.BAD_REQUEST )
                     .addObject( "simpleOntologyForm", SimpleOntologyForm.withInitialRows() );
         } catch ( IOException | ParseException e ) {
             log.warn( String.format( "Failed to import ontology from submitted form: %s.", importOntologyForm ), e );
-            bindingResult.reject( "AdminController.ImportOntologyForm.failedToParseOboFormat", new String[]{ importOntologyForm.getFilename(), e.getMessage() },
-                    String.format( "Failed to parse the ontology OBO format from %s: %s", importOntologyForm.getFilename(), e.getMessage() ) );
+            bindingResult.reject( "AdminController.ImportOntologyForm.failedToParseOboFormat", new String[]{ importOntologyForm.getFilename(), e.getMessage() }, null );
             return new ModelAndView( "admin/ontologies", HttpStatus.INTERNAL_SERVER_ERROR )
                     .addObject( "simpleOntologyForm", SimpleOntologyForm.withInitialRows() );
         }
@@ -711,7 +709,7 @@ public Object importReactomePathways( RedirectAttributes redirectAttributes ) {
         } catch ( ReactomeException e ) {
             log.error( "Failed to import Reactome pathways. Could this be an issue with the ontology configuration?", e );
             redirectAttributes.addFlashAttribute( "message", "Failed to import Reactome pathways: " + e.getMessage() + "." );
-            redirectAttributes.addFlashAttribute( "error", true );
+            redirectAttributes.addFlashAttribute( "error", Boolean.TRUE );
             return "redirect:/admin/ontologies";
         }
     }
@@ -730,7 +728,7 @@ public Object updateReactomePathways( @PathVariable(required = false) Ontology o
         } catch ( ReactomeException e ) {
             log.error( "Failed to update Reactome pathways. Could this be an issue with the ontology configuration?", e );
             redirectAttributes.addFlashAttribute( "message", "Failed to update Reactome pathways: " + e.getMessage() + "." );
-            redirectAttributes.addFlashAttribute( "error", true );
+            redirectAttributes.addFlashAttribute( "error", Boolean.TRUE );
             return "redirect:/admin/ontologies";
         }
     }
@@ -948,7 +946,7 @@ private Object activateOrDeactivateTerm( Ontology ontology,
      * Provides the ontology in OBO format.
      */
     @GetMapping(value = "/admin/ontologies/{ontology}/download", produces = "text/plain")
-    public ResponseEntity<StreamingResponseBody> downloadOntology( @PathVariable(required = false) Ontology ontology ) {
+    public ResponseEntity<StreamingResponseBody> downloadOntology( @PathVariable(required = false) Ontology ontology, TimeZone timeZone ) {
         if ( ontology == null ) {
             return ResponseEntity.notFound().build();
         }
@@ -957,7 +955,7 @@ public ResponseEntity<StreamingResponseBody> downloadOntology( @PathVariable(req
         headers.set( "Content-Disposition", String.format( "attachment; filename=%s.obo", ontology.getName() ) );
         return new ResponseEntity<>( outputStream -> {
             try ( Writer writer = new OutputStreamWriter( outputStream ) ) {
-                ontologyService.writeObo( ontology, writer );
+                ontologyService.writeObo( ontology, writer, timeZone );
             }
         }, headers, HttpStatus.OK );
     }
@@ -1002,7 +1000,7 @@ public Object move( @PathVariable(required = false) Ontology ontology, @RequestP
             d = OntologyService.Direction.DOWN;
         } else {
             return new ModelAndView( "admin/ontologies", HttpStatus.BAD_REQUEST )
-                    .addObject( "error", true )
+                    .addObject( "error", Boolean.TRUE )
                     .addObject( "message", String.format( "Invalid direction %s.", direction ) )
                     .addObject( "simpleOntologyForm", SimpleOntologyForm.withInitialRows() );
         }

src/main/java/ubc/pavlab/rdp/controllers/SearchController.java

@@ -114,7 +114,7 @@ public Object searchUsers( @Valid UserSearchParams userSearchParams, BindingResu
             } else {
                 modelAndView.addObject( "Invalid user search parameters." );
             }
-            modelAndView.addObject( "error", true );
+            modelAndView.addObject( "error", Boolean.TRUE );
             modelAndView.addObject( "users", Collections.emptyList() );
             if ( userSearchParams.isISearch() ) {
                 modelAndView.addObject( "itlUsers", Collections.emptyList() );
@@ -163,7 +163,7 @@ public ModelAndView searchUsersByName( @RequestParam String nameLike,
         if ( nameLike.isEmpty() ) {
             modelAndView.setStatus( HttpStatus.BAD_REQUEST );
             modelAndView.addObject( "message", "Researcher name cannot be empty." );
-            modelAndView.addObject( "error", true );
+            modelAndView.addObject( "error", Boolean.TRUE );
             modelAndView.addObject( "users", Collections.emptyList() );
             modelAndView.addObject( "itlUsers", Collections.emptyList() );
             modelAndView.addObject( "termsAvailabilityByApiUri", Collections.emptyMap() );
@@ -206,7 +206,7 @@ public ModelAndView searchUsersByDescription( @RequestParam String descriptionLi
         if ( descriptionLike.isEmpty() ) {
             modelAndView.setStatus( HttpStatus.BAD_REQUEST );
             modelAndView.addObject( "message", "Research interests cannot be empty." );
-            modelAndView.addObject( "error", true );
+            modelAndView.addObject( "error", Boolean.TRUE );
             modelAndView.addObject( "users", Collections.emptyList() );
             modelAndView.addObject( "itlUsers", Collections.emptyList() );
             modelAndView.addObject( "termsAvailabilityByApiUri", Collections.emptyMap() );
@@ -275,7 +275,7 @@ public ModelAndView searchUsersByGene( @RequestParam String symbol,
         if ( symbol.isEmpty() ) {
             modelAndView.setStatus( HttpStatus.BAD_REQUEST );
             modelAndView.addObject( "message", "Gene symbol cannot be empty." );
-            modelAndView.addObject( "error", true );
+            modelAndView.addObject( "error", Boolean.TRUE );
             return modelAndView;
         }
 

src/main/java/ubc/pavlab/rdp/listeners/OntologyListener.java

@@ -7,9 +7,9 @@
 import org.springframework.cache.CacheManager;
 import org.springframework.stereotype.Component;
 import org.springframework.transaction.event.TransactionalEventListener;
-import org.springframework.util.Assert;
 import ubc.pavlab.rdp.events.OnOntologyUpdateEvent;
 import ubc.pavlab.rdp.services.OntologyService;
+import ubc.pavlab.rdp.util.CacheUtils;
 
 /**
  * Listener for {@link ubc.pavlab.rdp.model.ontology.Ontology}-related events.
@@ -28,10 +28,8 @@ public class OntologyListener implements InitializingBean {
 
     @Override
     public void afterPropertiesSet() {
-        subtreeSizeCache = cacheManager.getCache( OntologyService.SUBTREE_SIZE_BY_TERM_CACHE_NAME );
-        Assert.notNull( subtreeSizeCache, String.format( "There is no cache named %s.", OntologyService.SIMPLE_ONTOLOGIES_CACHE_NAME ) );
-        simpleOntologiesCache = cacheManager.getCache( OntologyService.SUBTREE_SIZE_BY_TERM_CACHE_NAME );
-        Assert.notNull( simpleOntologiesCache, String.format( "There is no cache named %s.", OntologyService.SIMPLE_ONTOLOGIES_CACHE_NAME ) );
+        subtreeSizeCache = CacheUtils.getCache( cacheManager, OntologyService.SUBTREE_SIZE_BY_TERM_CACHE_NAME );
+        simpleOntologiesCache = CacheUtils.getCache( cacheManager, OntologyService.SUBTREE_SIZE_BY_TERM_CACHE_NAME );
     }
 
     @TransactionalEventListener

src/main/java/ubc/pavlab/rdp/model/Gene.java

@@ -19,7 +19,7 @@
 @Setter
 @EqualsAndHashCode(of = { "geneId" })
 @ToString(of = { "geneId", "symbol", "taxon" })
-public abstract class Gene {
+public abstract class Gene implements Serializable {
 
     @NaturalId
     @Column(name = "gene_id")

src/main/java/ubc/pavlab/rdp/model/GeneInfo.java

@@ -21,7 +21,7 @@
                 @Index(columnList = "gene_id, taxon_id"),
                 @Index(columnList = "symbol, taxon_id") })
 @Getter
-public class GeneInfo extends Gene implements Comparable<GeneInfo>, Serializable {
+public class GeneInfo extends Gene implements Comparable<GeneInfo> {
 
     public static Comparator<GeneInfo> getComparator() {
         return Comparator.comparing( GeneInfo::getGeneId );

src/main/java/ubc/pavlab/rdp/model/UserGene.java

@@ -43,7 +43,7 @@
 @CommonsLog
 @org.hibernate.annotations.Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
 @ToString(of = { "user", "tier", "privacyLevel" }, callSuper = true)
-public class UserGene extends Gene implements UserContent, Serializable {
+public class UserGene extends Gene implements UserContent {
 
     public static UserGeneBuilder builder( User user ) {
         return new UserGeneBuilder().user( user );

src/main/java/ubc/pavlab/rdp/model/ontology/OntologyTerm.java

@@ -1,7 +1,6 @@
 package ubc.pavlab.rdp.model.ontology;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
-import io.micrometer.core.lang.Nullable;
 import lombok.*;
 import lombok.experimental.SuperBuilder;
 import org.hibernate.annotations.NaturalId;
@@ -12,6 +11,7 @@
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.MappedSuperclass;
+import java.io.Serializable;
 import java.util.Locale;
 
 /**
@@ -26,7 +26,7 @@
 @EqualsAndHashCode(of = { "ontology", "termId" })
 @ToString(of = { "ontology", "termId", "name" })
 @SuperBuilder
-public abstract class OntologyTerm {
+public abstract class OntologyTerm implements Serializable {
 
     /**
      * Ontology to which is term is part of.

src/main/java/ubc/pavlab/rdp/model/ontology/OntologyTermInfo.java

@@ -11,7 +11,6 @@
 import org.springframework.context.support.DefaultMessageSourceResolvable;
 
 import javax.persistence.*;
-import java.io.Serializable;
 import java.text.Collator;
 import java.util.*;
 
@@ -35,7 +34,7 @@
 @ToString(of = { "id" }, callSuper = true)
 @org.hibernate.annotations.Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE)
 @SuperBuilder
-public class OntologyTermInfo extends OntologyTerm implements Serializable, Comparable<OntologyTermInfo> {
+public class OntologyTermInfo extends OntologyTerm implements Comparable<OntologyTermInfo> {
 
     /**
      * Maximum size of term ID and name.

src/main/java/ubc/pavlab/rdp/ontology/resolvers/OlsResolver.java

@@ -21,7 +21,7 @@ public class OlsResolver implements OntologyResolver {
 
     @Override
     public boolean accepts( Ontology ontology ) {
-        return ontology.getOntologyUrl() != null && ontology.getOntologyUrl().toString().startsWith( DEFAULT_IRI_PREFIX );
+        return ontology.getOntologyUrl() != null && ontology.getOntologyUrl().toExternalForm().startsWith( DEFAULT_IRI_PREFIX );
     }
 
     @Override
@@ -34,6 +34,6 @@ public URI resolveViewOntologyUrl( Ontology ontology ) {
     public URI resolveViewTermUrl( OntologyTerm term ) {
         return UriComponentsBuilder.fromHttpUrl( "https://www.ebi.ac.uk/ols/ontologies/{0}/terms" )
                 .queryParam( "iri", "{1}" )
-                .build( term.getOntology().getName(), DEFAULT_IRI_PREFIX + term.getTermId().replace( ":", "_" ) );
+                .build( term.getOntology().getName(), DEFAULT_IRI_PREFIX + term.getTermId().replace( ':', '_' ) );
     }
 }

src/main/java/ubc/pavlab/rdp/ontology/resolvers/OntobeeResolver.java

@@ -21,7 +21,7 @@ public class OntobeeResolver implements OntologyResolver {
 
     @Override
     public boolean accepts( Ontology ontology ) {
-        return ontology.getOntologyUrl().toString().startsWith( DEFAULT_IRI_PREFIX );
+        return ontology.getOntologyUrl().toExternalForm().startsWith( DEFAULT_IRI_PREFIX );
     }
 
     @Override
@@ -34,6 +34,6 @@ public URI resolveViewOntologyUrl( Ontology ontology ) {
     public URI resolveViewTermUrl( OntologyTerm term ) {
         return UriComponentsBuilder.fromHttpUrl( "https://ontobee.org/ontology/{0}" )
                 .queryParam( "iri", "{1}" )
-                .build( term.getOntology().getName().toUpperCase(), DEFAULT_IRI_PREFIX + term.getTermId().replace( ":", "_" ) );
+                .build( term.getOntology().getName().toUpperCase(), DEFAULT_IRI_PREFIX + term.getTermId().replace( ':', '_' ) );
     }
 }

src/main/java/ubc/pavlab/rdp/repositories/GeneOntologyTermInfoRepository.java

@@ -162,9 +162,14 @@ public Collection<GeneOntologyTermInfo> findAllById( Iterable<String> iterable )
     public Stream<GeneOntologyTermInfo> findAllAsStream() {
         Lock lock = rwLock.readLock();
         lock.lock();
-        return termsByIdOrAlias.values().stream()
-                .onClose( lock::unlock )
-                .distinct();
+        try {
+            return termsByIdOrAlias.values().stream()
+                    .onClose( lock::unlock )
+                    .distinct();
+        } catch ( Throwable t ) {
+            lock.unlock();
+            throw t;
+        }
     }
 
     /**

src/main/java/ubc/pavlab/rdp/services/GOServiceImpl.java

@@ -403,7 +403,7 @@ public Collection<Integer> getGenesInTaxon( String id, Taxon taxon ) {
         }
         return goRepository.findById( id )
                 .map( term -> getGenesInTaxon( term, taxon ) )
-                .orElse( Collections.emptySet() );
+                .orElseGet( Collections::emptySet );
     }
 
     @Override
@@ -535,7 +535,7 @@ private void evict( Iterable<GeneOntologyTermInfo> terms ) {
 
     private void evictAll() {
         log.debug( "Evicting all the terms from ancestors and descendants caches." );
-        ancestorsCache.clear();
-        descendantsCache.clear();
+        ancestorsCache.invalidate();
+        descendantsCache.invalidate();
     }
 }