Provide endpoint to return all genes (#86)

* Provide endpoint to return all genes

Co-authored-by: Calvin Lu <[email protected]>

src/main/java/org/mskcc/oncokb/transcript/repository/GeneRepository.java

@@ -1,5 +1,6 @@
 package org.mskcc.oncokb.transcript.repository;
 
+import java.util.List;
 import java.util.Optional;
 import org.mskcc.oncokb.transcript.domain.Gene;
 import org.springframework.cache.annotation.Cacheable;
@@ -17,4 +18,7 @@ public interface GeneRepository extends JpaRepository<Gene, Long> {
 
     @Cacheable(cacheResolver = "geneCacheResolver")
     Optional<Gene> findByHugoSymbol(String hugoSymbol);
+
+    @Query("select distinct g from Gene g left join fetch g.geneAliases ga left join fetch g.ensemblGenes eg")
+    List<Gene> findAllWithGeneAliasAndEnsemblGenes();
 }

src/main/java/org/mskcc/oncokb/transcript/service/GeneService.java

@@ -96,13 +96,15 @@ public Optional<Gene> partialUpdate(Gene gene) {
 
     /**
      * Get all the genes.
+     * We do not use the default find all is because the FetchType.EAGER in the gene model.
+     * The default will trigger a lot of queries to the database.
      *
      * @return the list of entities.
      */
     @Transactional(readOnly = true)
     public List<Gene> findAll() {
         log.debug("Request to get all Genes");
-        return geneRepository.findAll();
+        return geneRepository.findAllWithGeneAliasAndEnsemblGenes();
     }
 
     /**

src/main/java/org/mskcc/oncokb/transcript/web/rest/GeneResource.java

@@ -0,0 +1,36 @@
+package org.mskcc.oncokb.transcript.web.rest;
+
+import java.util.List;
+import org.mskcc.oncokb.transcript.domain.Gene;
+import org.mskcc.oncokb.transcript.service.GeneService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.*;
+
+/**
+ * REST controller for managing {@link org.mskcc.oncokb.transcript.domain.Gene}.
+ */
+@RestController
+@RequestMapping("/api")
+public class GeneResource {
+
+    private final Logger log = LoggerFactory.getLogger(GeneResource.class);
+
+    private final GeneService geneService;
+
+    public GeneResource(GeneService geneService) {
+        this.geneService = geneService;
+    }
+
+    /**
+     * {@code GET  /genes} : get all the genes.
+     *
+     * @return the {@link ResponseEntity} with status {@code 200 (OK)} and the list of genes in body.
+     */
+    @GetMapping("/genes")
+    public List<Gene> getAllGenes() {
+        log.debug("REST request to get all Genes");
+        return geneService.findAll();
+    }
+}