Merge branch 'hotfix-1.5.2'

docs/customization.md

@@ -324,6 +324,10 @@ rdp.ontologies.{ontologyName}.terms.{termName}.title
 rdp.ontologies.{ontologyName}.terms.{termName}.definition
 ```
 
+If your ontology/category is based on a [PURL](https://obofoundry.org/principles/fp-003-uris.html) source, its name will
+be rendered un uppercase. For example, "uberon" from http://purl.obolibrary.org/obo/uberon.obo will be displayed as
+"UBERON". You may override this by setting a custom title as described above.
+
 Note that we provide defaults for Reactome in the JAR package, so you must use custom messages for overriding those
 values. A warning will be displayed in the admin section if this is the case.
 

pom.xml

@@ -5,7 +5,7 @@
 
     <groupId>ubc.pavlab</groupId>
     <artifactId>rdp</artifactId>
-    <version>1.5.1</version>
+    <version>1.5.2</version>
 
     <description>
         Registry for model organism researchers, developed for the Canadian Rare Disease Models &amp; Mechanisms Network.
@@ -72,6 +72,11 @@
             <groupId>org.hibernate</groupId>
             <artifactId>hibernate-ehcache</artifactId>
         </dependency>
+        <!-- mentioned explicitly in CacheUtils for removeAll -->
+        <dependency>
+            <groupId>net.sf.ehcache</groupId>
+            <artifactId>ehcache</artifactId>
+        </dependency>
 
         <dependency>
             <groupId>org.springframework.boot</groupId>

src/main/java/ubc/pavlab/rdp/RemoteResourceConfig.java

@@ -17,8 +17,16 @@ public AsyncRestTemplate remoteResourceRestTemplate( ApplicationSettings applica
         SimpleClientHttpRequestFactory httpRequestFactory = new SimpleClientHttpRequestFactory();
         httpRequestFactory.setTaskExecutor( new SimpleAsyncTaskExecutor() );
         if ( applicationSettings.getIsearch().getRequestTimeout() != null ) {
+            log.warn( "The 'rdp.settings.isearch.request-timeout' configuration is deprecated." );
             httpRequestFactory.setConnectTimeout( 1000 );
             httpRequestFactory.setReadTimeout( (int) applicationSettings.getIsearch().getRequestTimeout().toMillis() );
+        } else {
+            if ( applicationSettings.getIsearch().getConnectTimeout() != null ) {
+                httpRequestFactory.setConnectTimeout( (int) applicationSettings.getIsearch().getConnectTimeout().toMillis() );
+            }
+            if ( applicationSettings.getIsearch().getReadTimeout() != null ) {
+                httpRequestFactory.setReadTimeout( (int) applicationSettings.getIsearch().getReadTimeout().toMillis() );
+            }
         }
         return new AsyncRestTemplate( httpRequestFactory );
     }

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

@@ -40,6 +40,14 @@ public static Comparator<GeneOntologyTermInfo> getComparator() {
     @JsonIgnore
     private MultiValueMap<Integer, Integer> directGeneIdsByTaxonId = new LinkedMultiValueMap<>();
 
+    /**
+     * Alias for {@link #getGoId()}.
+     */
+    @JsonIgnore
+    public String getId() {
+        return getGoId();
+    }
+
     /**
      * Obtain the size of the term as a number of genes in a taxon.
      * <p>

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

@@ -4,7 +4,10 @@
 import lombok.Getter;
 import lombok.Setter;
 import lombok.ToString;
+import org.apache.commons.lang3.StringUtils;
 import org.hibernate.annotations.NaturalId;
+import org.springframework.context.MessageSourceResolvable;
+import org.springframework.context.support.DefaultMessageSourceResolvable;
 
 import javax.persistence.Column;
 import javax.persistence.Lob;
@@ -28,4 +31,18 @@ public abstract class Organ {
     @Lob
     @Column(columnDefinition = "TEXT")
     private String description;
+
+    /**
+     * Obtain a resolvable title for this organ system.
+     */
+    public MessageSourceResolvable resolvableTitle() {
+        return new DefaultMessageSourceResolvable( new String[]{ "rdp.ontologies.uberon." + name + ".title" }, null, StringUtils.capitalize( name ) );
+    }
+
+    /**
+     * Obtain a resolvable definition for this organ system.
+     */
+    public MessageSourceResolvable resolvableDefinition() {
+        return new DefaultMessageSourceResolvable( new String[]{ "rdp.ontologies.uberon." + name + ".definition" }, null, description );
+    }
 }

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

@@ -2,6 +2,8 @@
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import io.swagger.v3.oas.annotations.media.Schema;
+import io.swagger.v3.oas.annotations.media.SchemaProperty;
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Data;
@@ -87,10 +89,12 @@ public String getFullName() {
     @Column(name = "privacy_level")
     private PrivacyLevelType privacyLevel;
 
+    @Schema(hidden = true)
     @JsonProperty(access = JsonProperty.Access.WRITE_ONLY)
     @Column(name = "shared", nullable = false)
     private boolean shared;
 
+    @Schema(hidden = true)
     @JsonProperty(access = JsonProperty.Access.WRITE_ONLY)
     @Column(name = "hide_genelist", nullable = false)
     private boolean hideGenelist;

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

@@ -4,6 +4,8 @@
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.annotation.JsonUnwrapped;
+import io.swagger.v3.oas.annotations.media.Schema;
+import io.swagger.v3.oas.annotations.media.SchemaProperty;
 import lombok.*;
 import lombok.extern.apachecommons.CommonsLog;
 import org.hibernate.annotations.CacheConcurrencyStrategy;
@@ -63,7 +65,9 @@ public static UserBuilder builder( Profile profile ) {
     }
 
     public static Comparator<User> getComparator() {
-        return Comparator.comparing( u -> u.getProfile().getFullName() );
+        return Comparator.comparing( ( User u ) -> u.getProfile().getFullName() )
+                .thenComparing( User::getEmail )
+                .thenComparing( User::getOriginUrl );
     }
 
     @Id
@@ -109,7 +113,7 @@ public static Comparator<User> getComparator() {
     private Timestamp modifiedAt;
 
     @Column(name = "enabled", nullable = false)
-    @JsonIgnore
+    @Schema(description = "This is deprecated: users exposed through the API are always enabled.", deprecated = true)
     private boolean enabled;
 
     /**

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

@@ -10,6 +10,7 @@
 import org.hibernate.annotations.NaturalId;
 import org.springframework.data.annotation.CreatedDate;
 import org.springframework.data.jpa.domain.support.AuditingEntityListener;
+import org.springframework.lang.Nullable;
 import ubc.pavlab.rdp.model.enums.PrivacyLevelType;
 import ubc.pavlab.rdp.model.enums.TierType;
 
@@ -61,6 +62,8 @@ public static UserGeneBuilder builder( User user ) {
     public static Comparator<UserGene> getComparator() {
         return Comparator.comparing( UserGene::getTaxon, Taxon.getComparator() )
                 .thenComparing( UserGene::getTier )
+                .thenComparing( UserGene::getSymbol )
+                .thenComparing( UserGene::getGeneId )
                 .thenComparing( UserGene::getUser, User.getComparator() );
     }
 
@@ -101,6 +104,7 @@ public static Comparator<UserGene> getComparator() {
     @JsonIgnore
     private Timestamp createdAt;
 
+    @Nullable
     @ManyToOne
     @JoinColumn(name = "gene_id", referencedColumnName = "gene_id", insertable = false, updatable = false, foreignKey = @ForeignKey(value = ConstraintMode.NO_CONSTRAINT))
     @JsonIgnore

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

@@ -15,6 +15,8 @@
 import java.util.SortedSet;
 import java.util.TreeSet;
 
+import static ubc.pavlab.rdp.util.PurlUtils.isPurl;
+
 /**
  * An ontology of terms.
  *
@@ -127,11 +129,21 @@ public int compareTo( Ontology ontology ) {
     /**
      * Obtain a resolvable for the title of this ontology.
      * <p>
-     * The default value is the upper case {@link #name}.
+     * The default value is the upper case {@link #name} if {@link #ontologyUrl} is set and is a
+     * <a href="https://obofoundry.org/principles/fp-003-uris.html">PURL</a>.
+     *
+     * @see ubc.pavlab.rdp.util.PurlUtils#isPurl(URL)
      */
     @JsonIgnore
     public DefaultMessageSourceResolvable getResolvableTitle() {
-        return new DefaultMessageSourceResolvable( new String[]{ "rdp.ontologies." + Ontology.this.getName() + ".title" }, name.toUpperCase() );
+        String defaultMessage;
+        if ( ontologyUrl != null && isPurl( ontologyUrl ) ) {
+            // this implies that the name is pulled from the OBO format, so its default value is not suitable for display
+            defaultMessage = name.toUpperCase();
+        } else {
+            defaultMessage = name;
+        }
+        return new DefaultMessageSourceResolvable( new String[]{ "rdp.ontologies." + name + ".title" }, defaultMessage );
     }
 
     /**
@@ -141,7 +153,8 @@ public DefaultMessageSourceResolvable getResolvableTitle() {
      * when calling {@link org.springframework.context.MessageSource#getMessage(MessageSourceResolvable, Locale)}.
      */
     @JsonIgnore
+
     public DefaultMessageSourceResolvable getResolvableDefinition() {
-        return new DefaultMessageSourceResolvable( new String[]{ "rdp.ontologies." + Ontology.this.getName() + ".definition" }, definition );
+        return new DefaultMessageSourceResolvable( new String[]{ "rdp.ontologies." + name + ".definition" }, definition );
     }
 }

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

@@ -8,6 +8,7 @@
 import org.springframework.context.support.DefaultMessageSourceResolvable;
 import org.springframework.data.annotation.CreatedDate;
 import org.springframework.data.jpa.domain.support.AuditingEntityListener;
+import org.springframework.lang.Nullable;
 import ubc.pavlab.rdp.model.User;
 import ubc.pavlab.rdp.model.UserContent;
 import ubc.pavlab.rdp.model.enums.PrivacyLevelType;
@@ -63,6 +64,7 @@ public static UserOntologyTerm fromOntologyTermInfo( User user, OntologyTermInfo
     /**
      * Original term from which this user term derived, if still available otherwise null.
      */
+    @Nullable
     @ManyToOne
     @JoinColumns(value = {
             @JoinColumn(name = "ontology_id", referencedColumnName = "ontology_id", insertable = false, updatable = false),

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

@@ -517,25 +517,18 @@ private void evict( Iterable<GeneOntologyTermInfo> terms ) {
                 .collect( Collectors.toSet() );
 
         // evict the terms from both caches
-        for ( GeneOntologyTermInfo term : termsToEvict ) {
-            ancestorsCache.evict( term );
-            descendantsCache.evict( term );
-        }
+        CacheUtils.evictAll( descendantsCache, termsToEvict );
 
         // all the ancestors mention one of the updated terms in their descendants, so we evict those
-        for ( GeneOntologyTermInfo ancestor : ancestors ) {
-            descendantsCache.evict( ancestor );
-        }
+        CacheUtils.evictAll( descendantsCache, ancestors );
 
         // conversely, all the descendants mention one of the updated term in their ancestors
-        for ( GeneOntologyTermInfo descendant : descendants ) {
-            ancestorsCache.evict( descendant );
-        }
+        CacheUtils.evictAll( ancestorsCache, descendants );
     }
 
     private void evictAll() {
         log.debug( "Evicting all the terms from ancestors and descendants caches." );
-        ancestorsCache.invalidate();
-        descendantsCache.invalidate();
+        ancestorsCache.clear();
+        descendantsCache.clear();
     }
 }

src/main/java/ubc/pavlab/rdp/settings/ApplicationSettings.java

@@ -217,9 +217,23 @@ public static class InternationalSearchSettings {
          * <p>
          * When formatted as a number, it is interpreted as a number of seconds. You may also use a unit suffix (i.e. '100ms')
          * to specify a precise amount of time.
+         *
+         * @deprecated use {@link #connectTimeout} and {@link #readTimeout} instead which provide more granularity in
+         * defining the timeout.
          */
+        @Deprecated
         @DurationUnit(value = ChronoUnit.SECONDS)
         private Duration requestTimeout;
+        /**
+         * Connection timeout in milliseconds, or null to disable.
+         */
+        @DurationUnit(value = ChronoUnit.MILLIS)
+        private Duration connectTimeout;
+        /**
+         * Read timeout in milliseconds, or null to disable.
+         */
+        @DurationUnit(value = ChronoUnit.MILLIS)
+        private Duration readTimeout;
     }
 
     @Data

src/main/java/ubc/pavlab/rdp/util/CacheUtils.java

@@ -1,8 +1,12 @@
 package ubc.pavlab.rdp.util;
 
+import net.sf.ehcache.Ehcache;
 import org.springframework.cache.Cache;
 import org.springframework.cache.CacheManager;
 
+import java.util.Collection;
+import java.util.Map;
+
 /**
  * Utilities for working with {@link CacheManager} and {@link Cache}.
  *
@@ -25,4 +29,22 @@ public static Cache getCache( CacheManager cacheManager, String cacheName ) thro
         }
         return cache;
     }
+
+    /**
+     * Evict all the given keys from the cache.
+     * <p>
+     * This takes advantage of cache-specific collection eviction such as {@link Ehcache#removeAll(Collection)}.
+     *
+     * @param cache cache from which keys are evicte
+     * @param keys  keys to be evicted
+     */
+    public static void evictAll( Cache cache, Collection<?> keys ) {
+        if ( cache.getNativeCache() instanceof Ehcache ) {
+            ( (Ehcache) cache.getNativeCache() ).removeAll( keys );
+        } else {
+            for ( Object key : keys ) {
+                cache.evict( key );
+            }
+        }
+    }
 }

src/main/java/ubc/pavlab/rdp/util/PurlResolver.java

@@ -18,19 +18,20 @@
 import java.net.MalformedURLException;
 import java.net.URL;
 
+import static ubc.pavlab.rdp.util.PurlUtils.isPurl;
+
 /**
  * Resolve resources from <a href="http://purl.obolibrary.org">purl.obolibrary.org</a>.
  *
  * @author poirigui
+ * @see PurlUtils
  */
 @CommonsLog
 public class PurlResolver implements ProtocolResolver {
 
-    private static final String PURL_PREFIX = "http://purl.obolibrary.org";
-
     @Override
     public Resource resolve( String location, ResourceLoader resourceLoader ) {
-        if ( !location.startsWith( PURL_PREFIX ) ) {
+        if ( !isPurl( location ) ) {
             return null;
         }
 

src/main/java/ubc/pavlab/rdp/util/PurlUtils.java

@@ -0,0 +1,19 @@
+package ubc.pavlab.rdp.util;
+
+import java.net.URL;
+
+/**
+ * Utilities to operate with <a href="https://obofoundry.org/principles/fp-003-uris.html">PURL</a>.
+ */
+public class PurlUtils {
+
+    private static final String PURL_PREFIX = "http://purl.obolibrary.org";
+
+    public static boolean isPurl( String url ) {
+        return url.startsWith( PURL_PREFIX );
+    }
+
+    public static boolean isPurl( URL url ) {
+        return isPurl( url.toExternalForm() );
+    }
+}

src/main/resources/application.properties

@@ -173,8 +173,9 @@ rdp.settings.isearch.user-id=
 #rdp.settings.isearch.search-token=
 ## Tokens for remote requests that authorize administrative access. Usually equal to the search-token, but can contain multiple entries separated by comma.
 rdp.settings.isearch.auth-tokens=
-## Timeout in seconds for remote search so that slow partners have limited incidence on search result speed.
-rdp.settings.isearch.request-timeout=3
+## Timeout in milliseconds for remote search connection and read so that slow partners have limited incidence on search result speed
+rdp.settings.isearch.connect-timeout=1000
+rdp.settings.isearch.read-timeout=3000
 
 # ontology settings
 rdp.settings.ontology.enabled=true

src/main/resources/static/js/model.js

@@ -120,7 +120,7 @@
                     }
                     row.push('<span class="align-middle">' +
                         '<a href="https://www.ebi.ac.uk/QuickGO/GTerm?id=' + encodeURIComponent(term.goId) + '" ' +
-                        'target="_blank" rel="noopener" data-toggle="tooltip" class="align-middle" title="' + term.definition + '">' + term.goId + '</a></span>');
+                        'target="_blank" rel="noopener" data-toggle="tooltip" data-boundary="window" class="align-middle" title="' + term.definition + '">' + term.goId + '</a></span>');
                     row.push('<span class="align-middle">' + term.name + '</span>');
                     row.push('<span class="align-middle">' + term.aspect + '</span>');
                     row.push('<a href="#" class="align-middle overlap-show-modal" data-toggle="modal" data-target="#overlapModal" data-go-id="' + term.goId + '">' + term.frequency + '</a>');