Issue #731 Metabolic pathways - species fix (#800)

epam · Mar 28, 2022 · f75dfe2 · f75dfe2
1 parent 84e95a3
commit f75dfe2
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/entity/pathway/PathwayQueryParams.java b/server/catgenome/src/main/java/com/epam/catgenome/entity/pathway/PathwayQueryParams.java
@@ -34,6 +34,6 @@ public class PathwayQueryParams {
     private PagingInfo pagingInfo;
     private String term;
     private PathwayDatabaseSource databaseSource;
-    private String species;
+    private Long taxId;
     private SortInfo sortInfo;
 }
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/manager/pathway/PathwayManager.java b/server/catgenome/src/main/java/com/epam/catgenome/manager/pathway/PathwayManager.java
@@ -455,9 +455,9 @@ private List<PathwayOrganism> getOrganisms(final Document doc) {
 
     private Query buildPathwaySearchQuery(final PathwayQueryParams params) throws ParseException {
         final String term = params.getTerm();
-        final String species = params.getSpecies();
+        final Long taxId = params.getTaxId();
         final PathwayDatabaseSource source = params.getDatabaseSource();
-        if (TextUtils.isBlank(term) && TextUtils.isBlank(species) && source == null) {
+        if (TextUtils.isBlank(term) && taxId == null && source == null) {
             return new MatchAllDocsQuery();
         }
 
@@ -478,8 +478,8 @@ private Query buildPathwaySearchQuery(final PathwayQueryParams params) throws Pa
             builder.add(termBuilder.build(), BooleanClause.Occur.MUST);
         }
 
-        if (!TextUtils.isBlank(species)) {
-            builder.add(buildQuery(PathwayIndexFields.SPECIES.getFieldName(), species, analyzer),
+        if (taxId != null) {
+            builder.add(buildQuery(PathwayIndexFields.SPECIES.getFieldName(), String.valueOf(taxId), analyzer),
                     BooleanClause.Occur.MUST);
         }
 

diff --git a/server/catgenome/src/test/java/com/epam/catgenome/manager/pathway/PathwayManagerTest.java b/server/catgenome/src/test/java/com/epam/catgenome/manager/pathway/PathwayManagerTest.java
@@ -108,6 +108,7 @@ public void loadPathways() throws IOException, ParseException {
         final PathwayQueryParams parameters = new PathwayQueryParams();
         final PagingInfo pagingInfo = new PagingInfo(2, 1);
         parameters.setPagingInfo(pagingInfo);
+        parameters.setTaxId(1L);
         final Page<NGBPathway> pathways = pathwayManager.loadPathways(parameters);
         pathwayManager.deletePathway(pathway.getPathwayId());
         pathwayManager.deletePathway(pathway1.getPathwayId());