Updates after merging with master branch

src/main/java/org/mskcc/oncokb/transcript/config/cache/LoggingCacheErrorHandler.java → src/main/java/org/mskcc/oncokb/curation/config/cache/LoggingCacheErrorHandler.java

@@ -1,4 +1,4 @@
-package org.mskcc.oncokb.transcript.config.cache;
+package org.mskcc.oncokb.curation.config.cache;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

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

@@ -21,7 +21,7 @@ public interface GeneRepository extends JpaRepository<Gene, Long>, JpaSpecificat
     @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")
+    @Query(value = "select distinct g from Gene g left join fetch g.geneAliases ga left join fetch g.ensemblGenes eg", nativeQuery = true)
     Page<Gene> findAllWithGeneAliasAndEnsemblGenes(Pageable pageable);
 
     @Query(

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

@@ -1,12 +1,28 @@
 package org.mskcc.oncokb.curation.web.rest;
 
+import java.net.URI;
+import java.net.URISyntaxException;
 import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
 import org.mskcc.oncokb.curation.domain.Gene;
+import org.mskcc.oncokb.curation.repository.GeneRepository;
+import org.mskcc.oncokb.curation.service.GeneQueryService;
 import org.mskcc.oncokb.curation.service.GeneService;
+import org.mskcc.oncokb.curation.service.criteria.GeneCriteria;
+import org.mskcc.oncokb.curation.web.rest.errors.BadRequestAlertException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
+import org.springframework.http.HttpHeaders;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.*;
+import org.springframework.web.servlet.support.ServletUriComponentsBuilder;
+import tech.jhipster.web.util.HeaderUtil;
+import tech.jhipster.web.util.PaginationUtil;
+import tech.jhipster.web.util.ResponseUtil;
 
 /**
  * REST controller for managing {@link org.mskcc.oncokb.curation.domain.Gene}.
@@ -17,20 +33,182 @@ public class GeneResource {
 
     private final Logger log = LoggerFactory.getLogger(GeneResource.class);
 
+    private static final String ENTITY_NAME = "gene";
+
+    @Value("${jhipster.clientApp.name}")
+    private String applicationName;
+
     private final GeneService geneService;
 
-    public GeneResource(GeneService geneService) {
+    private final GeneRepository geneRepository;
+
+    private final GeneQueryService geneQueryService;
+
+    public GeneResource(GeneService geneService, GeneRepository geneRepository, GeneQueryService geneQueryService) {
         this.geneService = geneService;
+        this.geneRepository = geneRepository;
+        this.geneQueryService = geneQueryService;
+    }
+
+    /**
+     * {@code POST  /genes} : Create a new gene.
+     *
+     * @param gene the gene to create.
+     * @return the {@link ResponseEntity} with status {@code 201 (Created)} and with body the new gene, or with status {@code 400 (Bad Request)} if the gene has already an ID.
+     * @throws URISyntaxException if the Location URI syntax is incorrect.
+     */
+    @PostMapping("/genes")
+    public ResponseEntity<Gene> createGene(@RequestBody Gene gene) throws URISyntaxException {
+        log.debug("REST request to save Gene : {}", gene);
+        if (gene.getId() != null) {
+            throw new BadRequestAlertException("A new gene cannot already have an ID", ENTITY_NAME, "idexists");
+        }
+        Gene result = geneService.save(gene);
+        return ResponseEntity
+            .created(new URI("/api/genes/" + result.getId()))
+            .headers(HeaderUtil.createEntityCreationAlert(applicationName, false, ENTITY_NAME, result.getId().toString()))
+            .body(result);
+    }
+
+    /**
+     * {@code PUT  /genes/:id} : Updates an existing gene.
+     *
+     * @param id the id of the gene to save.
+     * @param gene the gene to update.
+     * @return the {@link ResponseEntity} with status {@code 200 (OK)} and with body the updated gene,
+     * or with status {@code 400 (Bad Request)} if the gene is not valid,
+     * or with status {@code 500 (Internal Server Error)} if the gene couldn't be updated.
+     * @throws URISyntaxException if the Location URI syntax is incorrect.
+     */
+    @PutMapping("/genes/{id}")
+    public ResponseEntity<Gene> updateGene(@PathVariable(value = "id", required = false) final Long id, @RequestBody Gene gene)
+        throws URISyntaxException {
+        log.debug("REST request to update Gene : {}, {}", id, gene);
+        if (gene.getId() == null) {
+            throw new BadRequestAlertException("Invalid id", ENTITY_NAME, "idnull");
+        }
+        if (!Objects.equals(id, gene.getId())) {
+            throw new BadRequestAlertException("Invalid ID", ENTITY_NAME, "idinvalid");
+        }
+
+        if (!geneRepository.existsById(id)) {
+            throw new BadRequestAlertException("Entity not found", ENTITY_NAME, "idnotfound");
+        }
+
+        Gene result = geneService.save(gene);
+        return ResponseEntity
+            .ok()
+            .headers(HeaderUtil.createEntityUpdateAlert(applicationName, false, ENTITY_NAME, gene.getId().toString()))
+            .body(result);
+    }
+
+    /**
+     * {@code PATCH  /genes/:id} : Partial updates given fields of an existing gene, field will ignore if it is null
+     *
+     * @param id the id of the gene to save.
+     * @param gene the gene to update.
+     * @return the {@link ResponseEntity} with status {@code 200 (OK)} and with body the updated gene,
+     * or with status {@code 400 (Bad Request)} if the gene is not valid,
+     * or with status {@code 404 (Not Found)} if the gene is not found,
+     * or with status {@code 500 (Internal Server Error)} if the gene couldn't be updated.
+     * @throws URISyntaxException if the Location URI syntax is incorrect.
+     */
+    @PatchMapping(value = "/genes/{id}", consumes = { "application/json", "application/merge-patch+json" })
+    public ResponseEntity<Gene> partialUpdateGene(@PathVariable(value = "id", required = false) final Long id, @RequestBody Gene gene)
+        throws URISyntaxException {
+        log.debug("REST request to partial update Gene partially : {}, {}", id, gene);
+        if (gene.getId() == null) {
+            throw new BadRequestAlertException("Invalid id", ENTITY_NAME, "idnull");
+        }
+        if (!Objects.equals(id, gene.getId())) {
+            throw new BadRequestAlertException("Invalid ID", ENTITY_NAME, "idinvalid");
+        }
+
+        if (!geneRepository.existsById(id)) {
+            throw new BadRequestAlertException("Entity not found", ENTITY_NAME, "idnotfound");
+        }
+
+        Optional<Gene> result = geneService.partialUpdate(gene);
+
+        return ResponseUtil.wrapOrNotFound(
+            result,
+            HeaderUtil.createEntityUpdateAlert(applicationName, false, ENTITY_NAME, gene.getId().toString())
+        );
     }
 
     /**
      * {@code GET  /genes} : get all the genes.
      *
+     * @param pageable the pagination information.
+     * @param criteria the criteria which the requested entities should match.
      * @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();
+    public ResponseEntity<List<Gene>> getAllGenes(GeneCriteria criteria, Pageable pageable) {
+        log.debug("REST request to get Genes by criteria: {}", criteria);
+        Page<Gene> page = Page.empty();
+        if (criteria == null) {
+            page = geneService.findAll(pageable);
+        }
+        page = geneQueryService.findByCriteria(criteria, pageable);
+        HttpHeaders headers = PaginationUtil.generatePaginationHttpHeaders(ServletUriComponentsBuilder.fromCurrentRequest(), page);
+        return ResponseEntity.ok().headers(headers).body(page.getContent());
+    }
+
+    /**
+     * {@code GET  /genes/count} : count all the genes.
+     *
+     * @param criteria the criteria which the requested entities should match.
+     * @return the {@link ResponseEntity} with status {@code 200 (OK)} and the count in body.
+     */
+    @GetMapping("/genes/count")
+    public ResponseEntity<Long> countGenes(GeneCriteria criteria) {
+        log.debug("REST request to count Genes by criteria: {}", criteria);
+        return ResponseEntity.ok().body(geneQueryService.countByCriteria(criteria));
+    }
+
+    /**
+     * {@code GET  /genes/:id} : get the "id" gene.
+     *
+     * @param id the id of the gene to retrieve.
+     * @return the {@link ResponseEntity} with status {@code 200 (OK)} and with body the gene, or with status {@code 404 (Not Found)}.
+     */
+    @GetMapping("/genes/{id}")
+    public ResponseEntity<Gene> getGene(@PathVariable Long id) {
+        log.debug("REST request to get Gene : {}", id);
+        Optional<Gene> gene = geneService.findOne(id);
+        return ResponseUtil.wrapOrNotFound(gene);
+    }
+
+    /**
+     * {@code DELETE  /genes/:id} : delete the "id" gene.
+     *
+     * @param id the id of the gene to delete.
+     * @return the {@link ResponseEntity} with status {@code 204 (NO_CONTENT)}.
+     */
+    @DeleteMapping("/genes/{id}")
+    public ResponseEntity<Void> deleteGene(@PathVariable Long id) {
+        log.debug("REST request to delete Gene : {}", id);
+        geneService.delete(id);
+        return ResponseEntity
+            .noContent()
+            .headers(HeaderUtil.createEntityDeletionAlert(applicationName, false, ENTITY_NAME, id.toString()))
+            .build();
+    }
+
+    /**
+     * {@code SEARCH  /_search/genes?query=:query} : search for the gene corresponding
+     * to the query.
+     *
+     * @param query the query of the gene search.
+     * @param pageable the pagination information.
+     * @return the result of the search.
+     */
+    @GetMapping("/_search/genes")
+    public ResponseEntity<List<Gene>> searchGenes(@RequestParam String query, Pageable pageable) {
+        log.debug("REST request to search for a page of Genes for query {}", query);
+        Page<Gene> page = geneQueryService.findBySearchQuery(query, pageable);
+        HttpHeaders headers = PaginationUtil.generatePaginationHttpHeaders(ServletUriComponentsBuilder.fromCurrentRequest(), page);
+        return ResponseEntity.ok().headers(headers).body(page.getContent());
     }
 }

src/main/resources/config/application-dev.yml

@@ -15,10 +15,10 @@
 
 logging:
   level:
-    ROOT: DEBUG
-    tech.jhipster: DEBUG
-    org.hibernate.SQL: DEBUG
-    org.mskcc.oncokb.curation: DEBUG
+    ROOT: INFO
+    tech.jhipster: INFO
+    org.hibernate.SQL: INFO
+    org.mskcc.oncokb.curation: INFO
 
 spring:
   devtools: