Merge branch 'release-1.2.8'

Author: mbelmadani

pom.xml

@@ -5,7 +5,7 @@
 
     <groupId>ubc.pavlab</groupId>
     <artifactId>rdp</artifactId>
-    <version>1.2.7</version>
+    <version>1.2.8</version>
 
     <parent>
         <groupId>org.springframework.boot</groupId>

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

@@ -246,8 +246,13 @@ private boolean searchAuthorized(User user){
     }
 
     private Stats getStats() {
-        return new Stats( userService.countResearchers(), userGeneService.countUsersWithGenes(),
-                userGeneService.countAssociations(), userGeneService.countUniqueAssociations(),
+        return new Stats(
+                userService.countResearchers(),
+                userGeneService.countUsersWithGenes(),
+                userGeneService.countAssociations(),
+                userGeneService.countUniqueAssociations(),
+                userGeneService.countUniqueAssociationsAllTiers(),
+                userGeneService.countUniqueAssociationsToHumanAllTiers(),
                 userGeneService.researcherCountByTaxon() );
     }
 

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

@@ -43,6 +43,8 @@ public Map<String, Object> getAggregateStats(HttpServletResponse response) {
         stats.put( "researchers_registered_with_genes", userGeneService.countUsersWithGenes() );
         stats.put( "genes_added", userGeneService.countAssociations() );
         stats.put( "genes_added_unique", userGeneService.countUniqueAssociations() );
+        stats.put( "researchers_registered_with_genes_alltiers", userGeneService.countUniqueAssociationsAllTiers() );
+        stats.put( "human_genes_represented", userGeneService.countUniqueAssociationsToHumanAllTiers() );
         stats.put( "researcher_counts_by_taxon", userGeneService.researcherCountByTaxon() );
 
         return stats;

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

@@ -18,5 +18,7 @@ public class Stats {
     private Integer usersWithGenes;
     private Integer userGenes;
     private Integer uniqueUserGenes;
+    private Integer uniqueUserGenesTAll; // Unique genes added, counting all TIERs
+    private Integer uniqueUserGenesHumanTAll; // Unique genes mapped back to human, counting all TIERs
     private Map<String, Integer> researchersByTaxa;
 }

src/main/java/ubc/pavlab/rdp/model/enums/TierType.java

@@ -10,5 +10,5 @@ public enum TierType {
     TIER1, TIER2, TIER3, ANY, TIERS1_2;
 
     public static final Set<TierType> MANUAL_TIERS = EnumSet.of(TIER1, TIER2);
-
+    public static final Set<TierType> ALL_TIERS = EnumSet.of(TIER1, TIER2, TIER3, ANY);
 }

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

@@ -7,6 +7,7 @@
 import org.springframework.stereotype.Repository;
 import ubc.pavlab.rdp.model.Taxon;
 import ubc.pavlab.rdp.model.UserGene;
+import ubc.pavlab.rdp.model.Gene;
 import ubc.pavlab.rdp.model.enums.TierType;
 
 import javax.persistence.QueryHint;
@@ -43,4 +44,18 @@ public interface UserGeneRepository extends JpaRepository<UserGene, Integer> {
     @QueryHints(@QueryHint(name = "org.hibernate.cacheable", value = "true"))
     Collection<UserGene> findBySymbolContainingIgnoreCaseAndTaxonAndTierIn(String symbolContaining, Taxon taxon, Set<TierType> tiers);
 
+    // Return gene IDs of all associations in tiers
+    @QueryHints(@QueryHint(name = "org.hibernate.cacheable", value = "true"))
+    @Query("select distinct geneId FROM UserGene WHERE tier IN (:tiers)")
+    Collection<Integer> findDistinctGeneByTierIn( @Param("tiers") Collection<TierType> tiers );
+
+    // Return the reverse-mapped human gene(s) for a given ortholog target. 
+    @QueryHints(@QueryHint(name = "org.hibernate.cacheable", value = "true"))
+    @Query("select sourceGene FROM Ortholog where targetGene IN (:target_gene) ")
+    Collection<Integer> findHumanGenesForTarget(@Param("target_gene") Collection<Integer> targetGene);
+
+    // Return all human genes.
+    @QueryHints(@QueryHint(name = "org.hibernate.cacheable", value = "true"))
+    @Query("select geneId FROM UserGene where taxon = '9606'")
+    Collection<Integer> findAllHumanGenes();
 }

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

@@ -38,6 +38,8 @@ public interface UserGeneService {
     Map<String, Integer> researcherCountByTaxon();
 
     Integer countUsersWithGenes();
+    Integer countUniqueAssociationsAllTiers();
+    Integer countUniqueAssociationsToHumanAllTiers();
 
     Collection<Integer> findOrthologs(Integer source_gene, Integer targetTaxon);
 

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

@@ -80,6 +80,31 @@ public Integer countUsersWithGenes() {
         return userGeneRepository.countDistinctUser();
     }
 
+    @Cacheable(cacheNames = "stats", key = "#root.methodName")
+    @Override
+    public Integer countUniqueAssociationsAllTiers() {
+        return userGeneRepository.countDistinctGeneByTierIn( TierType.ALL_TIERS   );
+    }
+
+    @Cacheable(cacheNames = "stats", key = "#root.methodName")
+    @Override
+    public Integer countUniqueAssociationsToHumanAllTiers() {
+	/* This is also called the "human gene coverage" */
+
+        Collection<Integer> humanGenes = new HashSet<Integer>();
+
+        // Add orthologs mapped to humans
+        humanGenes.addAll( userGeneRepository.findHumanGenesForTarget(
+                userGeneRepository.findDistinctGeneByTierIn( TierType.ALL_TIERS   )
+        ));
+
+        // Add directly entered human genes
+        humanGenes.addAll( userGeneRepository.findAllHumanGenes() );
+
+        return humanGenes.size();
+    }
+
+    @Cacheable(cacheNames = "stats", key = "#root.methodName")
     @Override
     public Collection<Integer> findOrthologs( Integer sourceGene, Integer targetTaxon ) {
         return userGeneRepository.findOrthologs( sourceGene, targetTaxon );