Merge pull request #81 from nitin-ebi/recover-state

EVA-3474 Remove duplicate accessions when fetching from db
EBIvariation · Jan 12, 2024 · 9966bc2 · 9966bc2
2 parents fc07308 + b13dd5e
commit 9966bc2
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Showing 2 changed files with 15 additions and 8 deletions.
diff --git a/...i/ampt2d/commons/accession/service/BasicSpringDataRepositoryMonotonicDatabaseService.java b/...i/ampt2d/commons/accession/service/BasicSpringDataRepositoryMonotonicDatabaseService.java
@@ -28,7 +28,9 @@
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
@@ -62,18 +64,18 @@ public BasicSpringDataRepositoryMonotonicDatabaseService(
 
     @Override
     public long[] getAccessionsInRanges(Collection<MonotonicRange> ranges) {
-        List<Long> accessionsInDB = new ArrayList<>();
+        Set<Long> accessionsInDB = new HashSet<>();
         for (MonotonicRange potentiallyBigRange : ranges) {
             for (MonotonicRange range : ensureRangeMaxSize(potentiallyBigRange, MAX_RANGE_SIZE)) {
                 List<AccessionProjection<Long>> accessionsInRange =
                         repository.findByAccessionGreaterThanEqualAndAccessionLessThanEqual(range.getStart(),
                                 range.getEnd());
 
-                accessionsInDB.addAll(accessionsInRange.stream().map(ap -> ap.getAccession()).collect(Collectors.toList()));
+                accessionsInDB.addAll(accessionsInRange.stream().map(ap -> ap.getAccession()).collect(Collectors.toSet()));
             }
         }
 
-        long[] accessionArray = accessionsInDB.stream().mapToLong(l -> l).toArray();
+        long[] accessionArray = accessionsInDB.stream().mapToLong(l -> l).sorted().toArray();
         return accessionArray;
     }
 

diff --git a/.../ebi/ampt2d/commons/accession/core/BasicMonotonicAccessioningWithAlternateRangesTest.java b/.../ebi/ampt2d/commons/accession/core/BasicMonotonicAccessioningWithAlternateRangesTest.java
@@ -82,14 +82,19 @@ public void testRecoverState() {
 
         assertEquals(3, contiguousIdBlockService.getUncompletedBlocksByCategoryIdAndApplicationInstanceIdOrderByEndAsc(categoryId, instanceId2).size());
 
-        // create and save accessions in db (100 to 124)
-        List<AccessionWrapper<TestModel, String, Long>> accessions = LongStream.range(100l, 125l)
+        // create and save accessions in db (100 to 124) - save 2 sets of same accessions with different hashes
+        List<AccessionWrapper<TestModel, String, Long>> accessionsSet1 = LongStream.range(100l, 125l)
                 .boxed()
-                .map(longAcc -> new AccessionWrapper<>(longAcc, "hash" + longAcc, TestModel.of("test-obj-" + longAcc)))
+                .map(longAcc -> new AccessionWrapper<>(longAcc, "hash-1" + longAcc, TestModel.of("test-obj-1-" + longAcc)))
                 .collect(Collectors.toList());
-        databaseService.save(accessions);
+        List<AccessionWrapper<TestModel, String, Long>> accessionsSet2 = LongStream.range(100l, 125l)
+                .boxed()
+                .map(longAcc -> new AccessionWrapper<>(longAcc, "hash-2" + longAcc, TestModel.of("test-obj-2-" + longAcc)))
+                .collect(Collectors.toList());
+        databaseService.save(accessionsSet1);
+        databaseService.save(accessionsSet2);
 
-        // run recover blocks
+        // run recover state
         MonotonicAccessionGenerator generator = getGenerator(categoryId, instanceId2);
 
         // As we have already saved accessions in db from 100 to 124, the status should be