pass application instance id to generate accession

EBIvariation · Apr 26, 2024 · 67b73ef · 67b73ef
1 parent 777b892
commit 67b73ef
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Showing 19 changed files with 123 additions and 119 deletions.
diff --git a/...mmons-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/core/AccessioningService.java b/...mmons-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/core/AccessioningService.java
@@ -46,7 +46,7 @@ public interface AccessioningService<MODEL, HASH, ACCESSION> {
      * @return List of wrapper objects containing the accessioned objects and their associated accessions and hashes
      * @throws AccessionCouldNotBeGeneratedException when accession could not be generated
      */
-    List<GetOrCreateAccessionWrapper<MODEL, HASH, ACCESSION>> getOrCreate(List<? extends MODEL> messages)
+    List<GetOrCreateAccessionWrapper<MODEL, HASH, ACCESSION>> getOrCreate(List<? extends MODEL> messages, String applicationInstanceId)
             throws AccessionCouldNotBeGeneratedException;
 
     /**

diff --git a/...-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/core/BasicAccessioningService.java b/...-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/core/BasicAccessioningService.java
@@ -69,9 +69,10 @@ public BasicAccessioningService(AccessionGenerator<MODEL, ACCESSION> accessionGe
     }
 
     @Override
-    public List<GetOrCreateAccessionWrapper<MODEL, HASH, ACCESSION>> getOrCreate(List<? extends MODEL> messages)
+    public List<GetOrCreateAccessionWrapper<MODEL, HASH, ACCESSION>> getOrCreate(List<? extends MODEL> messages,
+                                                                                 String applicationInstanceId)
             throws AccessionCouldNotBeGeneratedException {
-        return saveAccessions(accessionGenerator.generateAccessions(mapHashOfMessages(messages)));
+        return saveAccessions(accessionGenerator.generateAccessions(mapHashOfMessages(messages), applicationInstanceId));
     }
 
     /**

diff --git a/...e/src/main/java/uk/ac/ebi/ampt2d/commons/accession/core/DecoratedAccessioningService.java b/...e/src/main/java/uk/ac/ebi/ampt2d/commons/accession/core/DecoratedAccessioningService.java
@@ -57,9 +57,9 @@ public DecoratedAccessioningService(AccessioningService<MODEL, HASH, DB_ACCESSIO
     }
 
     @Override
-    public List<GetOrCreateAccessionWrapper<MODEL, HASH, ACCESSION>> getOrCreate(List<? extends MODEL> messages)
+    public List<GetOrCreateAccessionWrapper<MODEL, HASH, ACCESSION>> getOrCreate(List<? extends MODEL> messages, String applicationInstanceId)
             throws AccessionCouldNotBeGeneratedException {
-        return getOrCreateDecorate(service.getOrCreate(messages));
+        return getOrCreateDecorate(service.getOrCreate(messages, applicationInstanceId));
     }
 
     private List<GetOrCreateAccessionWrapper<MODEL, HASH, ACCESSION>> getOrCreateDecorate(

diff --git a/...-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/generators/AccessionGenerator.java b/...-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/generators/AccessionGenerator.java
@@ -40,7 +40,7 @@ public interface AccessionGenerator<MODEL, ACCESSION> {
      * @return List of wrapper objects containing the accessioned objects and their associated accessions and hashes
      * @throws AccessionCouldNotBeGeneratedException when accession could not be generated
      */
-    <HASH> List<AccessionWrapper<MODEL, HASH, ACCESSION>> generateAccessions(Map<HASH, MODEL> messages)
+    <HASH> List<AccessionWrapper<MODEL, HASH, ACCESSION>> generateAccessions(Map<HASH, MODEL> messages, String applicationInstanceId)
             throws AccessionCouldNotBeGeneratedException;
 
     /**

diff --git a/...src/main/java/uk/ac/ebi/ampt2d/commons/accession/generators/SingleAccessionGenerator.java b/...src/main/java/uk/ac/ebi/ampt2d/commons/accession/generators/SingleAccessionGenerator.java
@@ -43,7 +43,7 @@ public SingleAccessionGenerator(Function<MODEL, ACCESSION> generateAccessionFunc
     }
 
     @Override
-    public <HASH> List<AccessionWrapper<MODEL, HASH, ACCESSION>> generateAccessions(Map<HASH, MODEL> messages) {
+    public <HASH> List<AccessionWrapper<MODEL, HASH, ACCESSION>> generateAccessions(Map<HASH, MODEL> messages, String applicationInstanceId) {
         return messages.entrySet()
                 .stream()
                 .map(entry -> new AccessionWrapper<>(generateAccessionFunction.apply(entry.getValue()), entry.getKey(),

diff --git a/...rc/main/java/uk/ac/ebi/ampt2d/commons/accession/rest/controllers/BasicRestController.java b/...rc/main/java/uk/ac/ebi/ampt2d/commons/accession/rest/controllers/BasicRestController.java
@@ -57,11 +57,12 @@ protected Function<MODEL, DTO> getModelToDTO() {
         return modelToDTO;
     }
 
-    @RequestMapping(method = RequestMethod.POST, produces = "application/json",
+    @RequestMapping(value = "/{applicationInstanceId}", method = RequestMethod.POST, produces = "application/json",
             consumes = "application/json")
     public List<GetOrCreateAccessionResponseDTO<DTO, MODEL, HASH, ACCESSION>> generateAccessions(
-            @RequestBody @Valid List<DTO> dtos) throws AccessionCouldNotBeGeneratedException {
-        return service.getOrCreate(dtos).stream()
+            @PathVariable String applicationInstanceId, @RequestBody @Valid List<DTO> dtos)
+            throws AccessionCouldNotBeGeneratedException {
+        return service.getOrCreate(dtos, applicationInstanceId).stream()
                 .map(accessionModel -> new GetOrCreateAccessionResponseDTO<>(accessionModel, modelToDTO))
                 .collect(Collectors.toList());
     }

diff --git a/...test/java/uk/ac/ebi/ampt2d/commons/accession/generators/SingleAccessionGeneratorTest.java b/...test/java/uk/ac/ebi/ampt2d/commons/accession/generators/SingleAccessionGeneratorTest.java
@@ -33,6 +33,7 @@
 import static org.junit.Assert.assertEquals;
 
 public class SingleAccessionGeneratorTest {
+    private static String APPLICATION_INSTANCE_ID = "TEST_APPPLICATION_INSTANCE_ID";
 
     private class TestUser {
 
@@ -56,7 +57,7 @@ public void testSingleAccessionGenerator() {
         hashToModel.put("hash1", new TestUser("test_name1", "test_surname1"));
         hashToModel.put("hash2", new TestUser("test_name2", "test_surname2"));
 
-        List<AccessionWrapper<TestUser, String, String>> accessions = generator.generateAccessions(hashToModel);
+        List<AccessionWrapper<TestUser, String, String>> accessions = generator.generateAccessions(hashToModel, APPLICATION_INSTANCE_ID);
         assertEquals(3, accessions.size());
         assertAccession(0, accessions, null);
     }
@@ -85,7 +86,7 @@ public void testOfHashAccession() {
         hashToModel.put("hash1", new TestUser("test_name1", "test_surname1"));
         hashToModel.put("hash2", new TestUser("test_name2", "test_surname2"));
 
-        List<AccessionWrapper<TestUser, String, String>> accessions = generator.generateAccessions(hashToModel);
+        List<AccessionWrapper<TestUser, String, String>> accessions = generator.generateAccessions(hashToModel, APPLICATION_INSTANCE_ID);
         assertEquals(3, accessions.size());
         assertAccession(0, accessions, new SHA1HashingFunction());
     }
@@ -101,7 +102,7 @@ public void testOfSHA1HashAccession() {
         hashToModel.put("hash1", new TestUser("test_name1", "test_surname1"));
         hashToModel.put("hash2", new TestUser("test_name2", "test_surname2"));
 
-        List<AccessionWrapper<TestUser, String, String>> accessions = generator.generateAccessions(hashToModel);
+        List<AccessionWrapper<TestUser, String, String>> accessions = generator.generateAccessions(hashToModel, APPLICATION_INSTANCE_ID);
         assertEquals(3, accessions.size());
         assertAccession(0, accessions, new SHA1HashingFunction());
     }
@@ -117,7 +118,7 @@ public void testPostSaveAction() {
         hashToModel.put("hash1", new TestUser("test_name1", "test_surname1"));
         hashToModel.put("hash2", new TestUser("test_name2", "test_surname2"));
 
-        List<AccessionWrapper<TestUser, String, String>> modelAccessions = generator.generateAccessions(hashToModel);
+        List<AccessionWrapper<TestUser, String, String>> modelAccessions = generator.generateAccessions(hashToModel, APPLICATION_INSTANCE_ID);
         Set<String> accessions = modelAccessions.stream().map(AccessionWrapper::getAccession).collect(Collectors.toSet());
         generator.postSave(new SaveResponse<>(accessions, new HashSet<>()));
     }

diff --git a/...a/src/test/java/uk/ac/ebi/ampt2d/commons/accession/core/BasicAccessioningServiceTest.java b/...a/src/test/java/uk/ac/ebi/ampt2d/commons/accession/core/BasicAccessioningServiceTest.java
@@ -48,7 +48,7 @@
 @DataJpaTest
 @ContextConfiguration(classes = {TestJpaDatabaseServiceTestConfiguration.class})
 public class BasicAccessioningServiceTest {
-
+    private static String APPLICATION_INSTANCE_ID = "TEST_APPPLICATION_INSTANCE_ID";
     @Autowired
     private TestRepository repository;
 
@@ -62,7 +62,7 @@ public void accessionNotRepeatedElements() throws AccessionCouldNotBeGeneratedEx
                         TestModel.of("service-test-1"),
                         TestModel.of("service-test-2"),
                         TestModel.of("service-test-3")
-                ));
+                ), APPLICATION_INSTANCE_ID);
         assertEquals(3, accessions.size());
     }
 
@@ -74,7 +74,7 @@ public void accessionWithRepeatedElementsReturnsUnique() throws AccessionCouldNo
                         TestModel.of("service-test-2"),
                         TestModel.of("service-test-2"),
                         TestModel.of("service-test-3")
-                ));
+                ), APPLICATION_INSTANCE_ID);
         assertEquals(3, accessions.size());
     }
 
@@ -94,7 +94,7 @@ public void getAlreadyGeneratedAccessionsReturnsGeneratedOnly() throws Accession
         accessioningService.getOrCreate(
                 Arrays.asList(
                         TestModel.of("service-test-3")
-                ));
+                ), APPLICATION_INSTANCE_ID);
 
         List<AccessionWrapper<TestModel, String, String>> accessions = accessioningService.get(Arrays.asList(
                 TestModel.of("service-test-1"),
@@ -111,13 +111,13 @@ public void accessioningMultipleTimesTheSameObjectReturnsTheSameAccession()
         List<GetOrCreateAccessionWrapper<TestModel, String, String>> accession1 = accessioningService.getOrCreate(
                 Arrays.asList(
                         TestModel.of("service-test-3")
-                ));
+                ), APPLICATION_INSTANCE_ID);
         TestTransaction.end();
 
         List<GetOrCreateAccessionWrapper<TestModel, String, String>> accession2 = accessioningService.getOrCreate(
                 Arrays.asList(
                         TestModel.of("service-test-3")
-                ));
+                ), APPLICATION_INSTANCE_ID);
         assertEquals(1, accession2.size());
         assertEquals(accession1.get(0).getAccession(), accession2.get(0).getAccession());
 
@@ -136,14 +136,14 @@ public void updateFailsWhenAccessionDoesNotExist() throws AccessionDoesNotExistE
     @Test(expected = HashAlreadyExistsException.class)
     public void updateFailsWhenAccessionAlreadyExists() throws AccessionDoesNotExistException,
             HashAlreadyExistsException, AccessionCouldNotBeGeneratedException, AccessionMergedException, AccessionDeprecatedException {
-        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-3"), TestModel.of("test-4")));
+        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-3"), TestModel.of("test-4")), APPLICATION_INSTANCE_ID);
         accessioningService.update("id-service-test-3", 1, TestModel.of("test-4"));
     }
 
     @Test
     public void testUpdate() throws AccessionDoesNotExistException,
             HashAlreadyExistsException, AccessionCouldNotBeGeneratedException, AccessionMergedException, AccessionDeprecatedException {
-        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-3")));
+        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-3")), APPLICATION_INSTANCE_ID);
         final AccessionVersionsWrapper<TestModel, String, String> updatedAccession =
                 accessioningService.update("id-service-test-3", 1, TestModel.of("test-3b"));
 
@@ -163,7 +163,7 @@ public void testUpdate() throws AccessionDoesNotExistException,
     @Test
     public void testPatch() throws AccessionCouldNotBeGeneratedException, AccessionDeprecatedException,
             AccessionDoesNotExistException, AccessionMergedException, HashAlreadyExistsException {
-        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-3")));
+        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-3")), APPLICATION_INSTANCE_ID);
         final AccessionVersionsWrapper<TestModel, String, String> accession =
                 accessioningService.patch("id-service-test-3", TestModel.of("test-3b"));
         assertEquals(2, accession.getModelWrappers().size());
@@ -182,7 +182,7 @@ public void testPatch() throws AccessionCouldNotBeGeneratedException, AccessionD
     @Test
     public void testGetAccessionVersion() throws AccessionCouldNotBeGeneratedException, AccessionDoesNotExistException,
             HashAlreadyExistsException, AccessionMergedException, AccessionDeprecatedException {
-        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-accession-version")));
+        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-accession-version")), APPLICATION_INSTANCE_ID);
         accessioningService.patch("id-service-test-accession-version", TestModel.of("test-accession-version-b"));
 
         final AccessionWrapper<TestModel, String, String> version1 = accessioningService
@@ -196,7 +196,7 @@ public void testGetAccessionVersion() throws AccessionCouldNotBeGeneratedExcepti
     @Test
     public void testDeprecate() throws AccessionCouldNotBeGeneratedException, AccessionMergedException,
             AccessionDoesNotExistException, AccessionDeprecatedException {
-        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-deprecate-version")));
+        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-deprecate-version")), APPLICATION_INSTANCE_ID);
         doDeprecateAndAssert("id-service-test-deprecate-version");
     }
 
@@ -220,15 +220,15 @@ public void testDeprecateAccessionDoesNotExist() throws AccessionCouldNotBeGener
     @Test(expected = AccessionDeprecatedException.class)
     public void testDeprecateTwice() throws AccessionCouldNotBeGeneratedException, AccessionMergedException,
             AccessionDoesNotExistException, AccessionDeprecatedException {
-        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-deprecate-version-2")));
+        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-deprecate-version-2")), APPLICATION_INSTANCE_ID);
         accessioningService.deprecate("id-service-test-deprecate-version-2", "Reasons");
         accessioningService.deprecate("id-service-test-deprecate-version-2", "Reasons");
     }
 
     @Test
     public void testDeprecateUpdated() throws AccessionCouldNotBeGeneratedException, AccessionMergedException,
             AccessionDoesNotExistException, AccessionDeprecatedException, HashAlreadyExistsException {
-        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-deprecate-update-version")));
+        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-deprecate-update-version")), APPLICATION_INSTANCE_ID);
         accessioningService.update("id-service-test-deprecate-update-version", 1,
                 TestModel.of("test-deprecate-update-version-updated!"));
         doDeprecateAndAssert("id-service-test-deprecate-update-version");
@@ -237,7 +237,7 @@ public void testDeprecateUpdated() throws AccessionCouldNotBeGeneratedException,
     @Test
     public void testDeprecatePatched() throws AccessionCouldNotBeGeneratedException, AccessionMergedException,
             AccessionDoesNotExistException, AccessionDeprecatedException, HashAlreadyExistsException {
-        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-deprecate-patch-version")));
+        accessioningService.getOrCreate(Arrays.asList(TestModel.of("test-deprecate-patch-version")), APPLICATION_INSTANCE_ID);
         accessioningService.patch("id-service-test-deprecate-patch-version",
                 TestModel.of("test-deprecate-update-version-patched!"));
         doDeprecateAndAssert("id-service-test-deprecate-patch-version");

diff --git a/...c/test/java/uk/ac/ebi/ampt2d/commons/accession/core/DecoratedAccessioningServiceTest.java b/...c/test/java/uk/ac/ebi/ampt2d/commons/accession/core/DecoratedAccessioningServiceTest.java
@@ -43,7 +43,7 @@
 @DataJpaTest
 @ContextConfiguration(classes = {TestJpaDatabaseServiceTestConfiguration.class})
 public class DecoratedAccessioningServiceTest {
-
+    private static String APPLICATION_INSTANCE_ID = "TEST_APPPLICATION_INSTANCE_ID";
     @Autowired
     private AccessioningService<TestModel, String, String> accessioningService;
 
@@ -52,7 +52,7 @@ public void assertGetOrCreate() throws AccessionCouldNotBeGeneratedException {
         List<GetOrCreateAccessionWrapper<TestModel, String, String>> accessions = getPrefixedService().getOrCreate(
                 Arrays.asList(
                         TestModel.of("service-test-1")
-                ));
+                ), APPLICATION_INSTANCE_ID);
         assertEquals(1, accessions.size());
         assertEquals("prefix-id-service-service-test-1", accessions.get(0).getAccession());
     }
@@ -138,7 +138,7 @@ public void assertMerge() throws AccessionMergedException, AccessionDoesNotExist
                 Arrays.asList(
                         TestModel.of("service-test-1"),
                         TestModel.of("service-test-2")
-                ));
+                ), APPLICATION_INSTANCE_ID);
         assertEquals(2, accessions.size());
         getPrefixedService().merge("prefix-id-service-service-test-1", "prefix-id-service-service-test-2", "reason");
     }

diff --git a/.../uk/ac/ebi/ampt2d/commons/accession/generators/monotonic/MonotonicAccessionGenerator.java b/.../uk/ac/ebi/ampt2d/commons/accession/generators/monotonic/MonotonicAccessionGenerator.java
@@ -45,19 +45,16 @@ public class MonotonicAccessionGenerator<MODEL> implements AccessionGenerator<MO
 
     private final BlockManager blockManager;
     private final String categoryId;
-    private final String applicationInstanceId;
     private final ContiguousIdBlockService blockService;
     private MonotonicDatabaseService monotonicDatabaseService;
 
     private boolean SHUTDOWN = false;
     private boolean RUN_RECOVERY = true;
 
     public MonotonicAccessionGenerator(String categoryId,
-                                       String applicationInstanceId,
                                        ContiguousIdBlockService contiguousIdBlockService,
                                        MonotonicDatabaseService monotonicDatabaseService) {
         this.categoryId = categoryId;
-        this.applicationInstanceId = applicationInstanceId;
         this.blockService = contiguousIdBlockService;
         this.monotonicDatabaseService = monotonicDatabaseService;
         assertBlockParametersAreInitialized(blockService, categoryId);
@@ -70,7 +67,7 @@ private static void assertBlockParametersAreInitialized(ContiguousIdBlockService
         }
     }
 
-    private void recoverState() {
+    private void recoverState(String applicationInstanceId) {
         if (RUN_RECOVERY && monotonicDatabaseService != null) {
             List<ContiguousIdBlock> uncompletedBlocks = blockService
                     .reserveUncompletedBlocksForCategoryIdAndApplicationInstanceId(categoryId, applicationInstanceId);
@@ -103,12 +100,12 @@ private void recoverStateForElements(long[] committedElements) throws AccessionI
         blockService.save(blockManager.recoverState(committedElements));
     }
 
-    public synchronized long[] generateAccessions(int numAccessionsToGenerate)
+    public synchronized long[] generateAccessions(int numAccessionsToGenerate, String applicationInstanceId)
             throws AccessionCouldNotBeGeneratedException {
         checkAccessionGeneratorNotShutDown();
-        recoverState();
+        recoverState(applicationInstanceId);
         long[] accessions = new long[numAccessionsToGenerate];
-        reserveNewBlocksUntilSizeIs(numAccessionsToGenerate);
+        reserveNewBlocksUntilSizeIs(numAccessionsToGenerate, applicationInstanceId);
 
         int i = 0;
         while (i < numAccessionsToGenerate) {
@@ -127,7 +124,7 @@ public synchronized long[] generateAccessions(int numAccessionsToGenerate)
      *
      * @param totalAccessionsToGenerate
      */
-    private synchronized void reserveNewBlocksUntilSizeIs(int totalAccessionsToGenerate) {
+    private synchronized void reserveNewBlocksUntilSizeIs(int totalAccessionsToGenerate, String applicationInstanceId) {
         while (!blockManager.hasAvailableAccessions(totalAccessionsToGenerate)) {
             ExponentialBackOff.execute(() -> reserveNewBlock(categoryId, applicationInstanceId), 10, 30);
         }
@@ -153,10 +150,10 @@ public synchronized MonotonicRangePriorityQueue getAvailableRanges() {
     }
 
     @Override
-    public <HASH> List<AccessionWrapper<MODEL, HASH, Long>> generateAccessions(Map<HASH, MODEL> messages)
+    public <HASH> List<AccessionWrapper<MODEL, HASH, Long>> generateAccessions(Map<HASH, MODEL> messages, String applicationInstanceId)
             throws AccessionCouldNotBeGeneratedException {
         checkAccessionGeneratorNotShutDown();
-        long[] accessions = generateAccessions(messages.size());
+        long[] accessions = generateAccessions(messages.size(), applicationInstanceId);
         int i = 0;
         List<AccessionWrapper<MODEL, HASH, Long>> accessionedModels = new ArrayList<>();
         for (Map.Entry<HASH, ? extends MODEL> entry : messages.entrySet()) {