Remove rest of CRUD operations from BrAPIGermplasmDAO

src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java

@@ -69,17 +69,12 @@ public class BrAPIGermplasmDAO {
     @Property(name = "brapi.server.reference-source")
     private String referenceSource;
 
-    @Property(name = "micronaut.bi.api.run-scheduled-tasks")
-    private boolean runScheduledTasks;
-
     @Property(name = "brapi.paginate.germplasm")
     private boolean paginateGermplasm;
 
     @Property(name = "data-table.max-size")
     private int dataTableMaxSize;
 
-    private final ProgramCache<BrAPIGermplasm> programGermplasmCache;
-
     private final BrAPIEndpointProvider brAPIEndpointProvider;
 
     private final int brapiMaxPageSize;
@@ -88,30 +83,15 @@ public class BrAPIGermplasmDAO {
     public BrAPIGermplasmDAO(ProgramDAO programDAO,
                              ImportDAO importDAO,
                              BrAPIDAOUtil brAPIDAOUtil,
-                             ProgramCacheProvider programCacheProvider,
                              BrAPIEndpointProvider brAPIEndpointProvider,
                              @Property(name = "brapi.cache.fetch-page-size") int brapiFetchPageSize) {
         this.programDAO = programDAO;
         this.importDAO = importDAO;
         this.brAPIDAOUtil = brAPIDAOUtil;
-        this.programGermplasmCache = programCacheProvider.getProgramCache(this::fetchProgramGermplasm, BrAPIGermplasm.class);
         this.brAPIEndpointProvider = brAPIEndpointProvider;
         this.brapiMaxPageSize = brapiFetchPageSize;
     }
 
-    @Scheduled(initialDelay = "${startup.delay.germplasm}")
-    public void setup() {
-        if(!runScheduledTasks) {
-            return;
-        }
-        // Populate germplasm cache for all programs on startup
-        log.debug("populating germplasm cache");
-        List<Program> programs = programDAO.getActive();
-        if(programs != null) {
-            programGermplasmCache.populate(programs.stream().map(Program::getId).collect(Collectors.toList()));
-        }
-    }
-
     /**
      * Fetch the germplasm for this program, and process it to remove storage specific values
      * @param programId
@@ -203,9 +183,6 @@ private Map<String, BrAPIGermplasm> fetchProgramGermplasm(UUID programId) throws
         }
     }
 
-    public void repopulateGermplasmCacheForProgram(UUID programId) {
-        programGermplasmCache.populate(programId);
-    }
     /**
      * Process germplasm into a format for display
      * @param programGermplasm
@@ -487,11 +464,8 @@ public List<BrAPIGermplasm> updateBrAPIGermplasm(List<BrAPIGermplasm> putBrAPIGe
         var program = new Program(programDAO.fetchOneById(programId));
         try {
             if (!putBrAPIGermplasmList.isEmpty()) {
-                Callable<Map<String, BrAPIGermplasm>> postFunction = () -> {
-                    List<BrAPIGermplasm> putResponse = putGermplasm(putBrAPIGermplasmList, api);
-                    return processGermplasmForDisplay(putResponse, program);
-                };
-                return programGermplasmCache.post(programId, postFunction);
+                List<BrAPIGermplasm> putResponse = putGermplasm(putBrAPIGermplasmList, api);
+                return new ArrayList<>(processGermplasmForDisplay(putResponse, program).values());
             }
             return new ArrayList<>();
         } catch (Exception e) {

src/main/java/org/breedinginsight/brapps/importer/services/processors/germplasm/GermplasmProcessor.java

@@ -724,8 +724,6 @@ public void postBrapiData(Map<Integer, PendingImport> mappedBrAPIImport, Program
             try {
                 // Create germplasm list
                 brAPIListDAO.createBrAPILists(List.of(importList), program.getId(), upload);
-                // Now that we have finished uploading, fetch all the data posted to BrAPI to the cache so it is up-to-date.
-                brAPIGermplasmDAO.repopulateGermplasmCacheForProgram(program.getId());
             } catch (ApiException e) {
                 throw new InternalServerException(e.toString(), e);
             }

src/test/java/org/breedinginsight/brapps/importer/GermplasmFileImportTest.java

@@ -1257,8 +1257,5 @@ private void seedExistingGermplasm(String accessionNumber, String displayName, S
         germplasm.setExternalReferences(externalReferences);
 
         germplasmDAO.createBrAPIGermplasm(List.of(germplasm), validProgram.getId(), null);
-
-        //Refresh cache so importer lookup sees the seeded germplasm immediately.
-        germplasmDAO.repopulateGermplasmCacheForProgram(validProgram.getId());
     }
 }

src/test/java/org/breedinginsight/services/BrAPIGermplasmServiceUnitTest.java

@@ -51,7 +51,6 @@ public class BrAPIGermplasmServiceUnitTest extends DatabaseTest {
     private BrAPIGermplasmService germplasmService;
     private BrAPIDAOUtil brAPIDAOUtil;
     private String referenceSource;
-    private ProgramCacheProvider cacheProvider;
 
     @SneakyThrows
     @BeforeEach
@@ -61,8 +60,7 @@ void setup() {
         listDAO = mock(BrAPIListDAO.class);
         programDAO = mock(ProgramDAO.class);
         brAPIDAOUtil = mock(BrAPIDAOUtil.class);
-        cacheProvider = new ProgramCacheProvider(super.getRedisConnection());
-        germplasmDAO = new BrAPIGermplasmDAO(programDAO, mock(ImportDAO.class), brAPIDAOUtil, cacheProvider, new BrAPIEndpointProvider(), 65000);
+        germplasmDAO = new BrAPIGermplasmDAO(programDAO, mock(ImportDAO.class), brAPIDAOUtil, new BrAPIEndpointProvider(), 65000);
         programService = mock(ProgramService.class);
 
         Field externalReferenceSource = BrAPIGermplasmDAO.class.getDeclaredField("referenceSource");
@@ -157,11 +155,6 @@ public void getGermplasmListExport() {
                 any(GermplasmQueryParams.class))).thenReturn(germplasm);
         when(brAPIDAOUtil.getBrAPIProgramDbId(any())).thenReturn(brapiProgramDbId);
 
-        //Create germplasm cache of stub data
-        Method setupMethod = BrAPIGermplasmDAO.class.getDeclaredMethod("setup");
-        setupMethod.setAccessible(true);
-        setupMethod.invoke(germplasmDAO);
-
         //Create test instance of service, injecting spy- and mock-dependencies
         germplasmService = new BrAPIGermplasmService(brAPIListSpy, programSpy, germplasmDAO);