Merge pull request #21 from alliance-genome/fix_annotation_search

Fixed annotation search
alliance-genome · Aug 26, 2021 · 2ef9dc0 · 2ef9dc0
2 parents a2d9937 + 5281111
commit 2ef9dc0
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Showing 6 changed files with 38 additions and 22 deletions.
diff --git a/src/main/cliapp/src/components/DiseaseAnnotationsComponent.js b/src/main/cliapp/src/components/DiseaseAnnotationsComponent.js
@@ -29,11 +29,11 @@ export const DiseaseAnnotationsComponent = () => {
       setDiseaseAnnotations(data.results);
       setTotalRecords(data.totalResults);
     },
-      onError: (error) => {
-          errorMessage.current.show([
-              { severity: 'error', summary: 'Error', detail: error.message, sticky: true }
-          ])
-      },
+    onError: (error) => {
+      errorMessage.current.show([
+        { severity: 'error', summary: 'Error', detail: error.message, sticky: true }
+      ])
+    },
     keepPreviousData: true
 
   })
@@ -72,7 +72,7 @@ export const DiseaseAnnotationsComponent = () => {
 
   const publicationTemplate = (rowData) => {
     if (rowData) {
-      return <div>{rowData.referenceList[0].curie}</div>
+      return <div>{rowData.referenceList.map(a => a.curie)}</div>
     }
   };
 
@@ -82,8 +82,8 @@ export const DiseaseAnnotationsComponent = () => {
   return (
     <div>
       <div className="card">
-          <h3>Disease Annotations Table</h3>
-          <Messages ref={errorMessage}/>
+        <h3>Disease Annotations Table</h3>
+        <Messages ref={errorMessage}/>
         <DataTable value={diseaseAnnotations} className="p-datatable-md"
           sortMode="multiple" removableSort onSort={onSort} multiSortMeta={multiSortMeta}
           first={first} onFilter={onFilter} filters={filters}
@@ -92,10 +92,10 @@ export const DiseaseAnnotationsComponent = () => {
           paginatorTemplate="CurrentPageReport FirstPageLink PrevPageLink PageLinks NextPageLink LastPageLink RowsPerPageDropdown"
           currentPageReportTemplate="Showing {first} to {last} of {totalRecords}" rows={rows} rowsPerPageOptions={[10, 20, 50, 100, 250, 1000]}
           paginatorLeft={paginatorLeft} paginatorRight={paginatorRight}>
-          <Column field="id" header="Id" sortable filter ></Column>
+          <Column field="id" header="Id" sortable ></Column>
           <Column field="subject.curie" header="Subject" sortable filter ></Column>
           <Column field="object.curie" header="Disease" sortable filter ></Column>
-          <Column field="referenceList" header="Reference" body={publicationTemplate} sortable filter ></Column>
+          <Column field="referenceList.curie" header="Reference" body={publicationTemplate} sortable filter ></Column>
         </DataTable>
       </div>
     </div>

diff --git a/src/main/cliapp/src/components/FMSComponent.js b/src/main/cliapp/src/components/FMSComponent.js
@@ -22,7 +22,8 @@ export const FMSComponent = () => {
     fmsService.getReleases().then(results => {
       console.log(results);
       setReleases(results.reverse());
-      //selectedRelease = results[0].releaseVersion;
+      //selectedRelease = results[0].releaseVersio;
+      //setSelectedRelease(results[0].releaseVersion);
       //setDataFiles(results.dataFiles);
     });
 

diff --git a/src/main/cliapp/src/service/DiseaseService.js b/src/main/cliapp/src/service/DiseaseService.js
@@ -2,25 +2,27 @@ import axios from 'axios';
 
 export class DiseaseService {
     getDiseases(limit, page, sorts, filters) {
-
         var sortOptions = {};
 
         var sortArray = {};
-        sorts.forEach((o) => {
+        if(sorts) { 
+          sorts.forEach((o) => {
             sortArray[o.field] = o.order;
-        });
+          });
+        }
 
         var filterArray = {};
-
-        Object.keys(filters).forEach((key) => {
+        if(filters) {
+          Object.keys(filters).forEach((key) => {
             filterArray[key] = filters[key]["value"];
-        });
+          });
+        }
 
         if(Object.keys(filterArray).length > 0) {
-            sortOptions["searchFilters"] = filterArray;
+          sortOptions["searchFilters"] = filterArray;
         }
         if(Object.keys(sortArray).length > 0) {
-            sortOptions["sortOrders"] = sortArray;
+          sortOptions["sortOrders"] = sortArray;
         }
 
         return axios.post('/api/doterm/search?limit=' + limit + '&page=' + page, sortOptions).then(res => res.data);

diff --git a/src/main/java/org/alliancegenome/curation_api/base/BaseGeneratedEntity.java b/src/main/java/org/alliancegenome/curation_api/base/BaseGeneratedEntity.java
@@ -6,6 +6,7 @@
 
 import org.alliancegenome.curation_api.view.View;
 import org.hibernate.annotations.*;
+import org.hibernate.search.engine.backend.types.*;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.*;
 
 import com.fasterxml.jackson.annotation.JsonView;
@@ -15,8 +16,8 @@
 @Data @EqualsAndHashCode(callSuper = false)
 @MappedSuperclass
 public class BaseGeneratedEntity extends BaseEntity {
-    
-    @Id
+
+    @Id @DocumentId
     @GeneratedValue(strategy = GenerationType.SEQUENCE)
     @JsonView({View.FieldsOnly.class})
     private Long id;

diff --git a/src/main/java/org/alliancegenome/curation_api/base/BaseSQLDAO.java b/src/main/java/org/alliancegenome/curation_api/base/BaseSQLDAO.java
@@ -140,8 +140,9 @@ public SearchResults<E> searchByParams(Pagination pagination, Map<String, Object
                 })
                 .toQuery();
 
-        SearchResult<E> result = query.fetch(pagination.getPage() * pagination.getLimit(), pagination.getLimit());
         log.debug(query);
+        SearchResult<E> result = query.fetch(pagination.getPage() * pagination.getLimit(), pagination.getLimit());
+
 
         SearchResults<E> results = new SearchResults<E>();
         results.setResults(result.hits());

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/Association.java b/src/main/java/org/alliancegenome/curation_api/model/entities/Association.java
@@ -9,6 +9,10 @@
 import org.alliancegenome.curation_api.view.View;
 import org.eclipse.microprofile.openapi.annotations.media.Schema;
 import org.hibernate.envers.Audited;
+import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.*;
+import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.*;
 
 import com.fasterxml.jackson.annotation.JsonView;
 
@@ -22,13 +26,20 @@
 @Schema(name = "association", description = "Annotation class representing a disease annotation")
 public class Association extends BaseGeneratedEntity {
 
+    @IndexedEmbedded(includeDepth = 1)
+    @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
     @ManyToOne
     @JsonView({View.FieldsOnly.class})
     private BiologicalEntity subject;
+
+    @IndexedEmbedded(includeDepth = 1)
+    @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
     @ManyToOne
     @JsonView({View.FieldsOnly.class})
     private DOTerm object;
 
+    @IndexedEmbedded(includeDepth = 1)
+    @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
     @ManyToMany
     @JsonView({View.FieldsOnly.class})
     private List<Reference> referenceList;