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EVA-3554 Pass application instance id to generate accession #87

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May 1, 2024
Merged

EVA-3554 Pass application instance id to generate accession #87

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67b73ef
pass application instance id to generate accession
nitin-ebi Apr 26, 2024
474364d
fix testt
nitin-ebi Apr 26, 2024
2a07f2c
fix test
nitin-ebi Apr 26, 2024
0749b6c
review comments
nitin-ebi Apr 26, 2024
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2 changes: 1 addition & 1 deletion ...mmons-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/core/AccessioningService.java
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Expand Up @@ -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)
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Can you update the method comment to explain what is the applicationInstanceId and why we're passing it ?

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Also I'm wondering if we should avoid reusing the variable applicationInstanceId in case there are still beans that would populate it from the properties file.

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Added the comment.
As These are parameter variables and not instance variables of a class, these would not get populated automatically.

throws AccessionCouldNotBeGeneratedException;

/**
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5 changes: 3 additions & 2 deletions ...-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/core/BasicAccessioningService.java
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Expand Up @@ -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));
}

/**
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4 changes: 2 additions & 2 deletions ...e/src/main/java/uk/ac/ebi/ampt2d/commons/accession/core/DecoratedAccessioningService.java
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Expand Up @@ -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(
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2 changes: 1 addition & 1 deletion ...-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/generators/AccessionGenerator.java
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Expand Up @@ -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;

/**
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2 changes: 1 addition & 1 deletion ...src/main/java/uk/ac/ebi/ampt2d/commons/accession/generators/SingleAccessionGenerator.java
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Expand Up @@ -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(),
Expand Down
7 changes: 4 additions & 3 deletions ...rc/main/java/uk/ac/ebi/ampt2d/commons/accession/rest/controllers/BasicRestController.java
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Expand Up @@ -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());
}
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9 changes: 5 additions & 4 deletions ...test/java/uk/ac/ebi/ampt2d/commons/accession/generators/SingleAccessionGeneratorTest.java
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Expand Up @@ -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 {

Expand All @@ -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);
}
Expand Down Expand Up @@ -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());
}
Expand All @@ -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());
}
Expand All @@ -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<>()));
}
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28 changes: 14 additions & 14 deletions ...a/src/test/java/uk/ac/ebi/ampt2d/commons/accession/core/BasicAccessioningServiceTest.java
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Expand Up @@ -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;

Expand All @@ -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());
}

Expand All @@ -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());
}

Expand All @@ -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"),
Expand All @@ -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());

Expand All @@ -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"));

Expand All @@ -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());
Expand All @@ -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
Expand All @@ -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");
}

Expand All @@ -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");
Expand All @@ -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");
Expand Down
6 changes: 3 additions & 3 deletions ...c/test/java/uk/ac/ebi/ampt2d/commons/accession/core/DecoratedAccessioningServiceTest.java
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Expand Up @@ -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;

Expand All @@ -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());
}
Expand Down Expand Up @@ -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");
}
Expand Down
2 changes: 1 addition & 1 deletion ...ns-jpa/src/test/java/uk/ac/ebi/ampt2d/commons/accession/rest/BasicRestControllerTest.java
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Expand Up @@ -92,7 +92,7 @@ public void testAccessionOk() throws Exception {
private ResultActions doAccession(ResultMatcher resultMatcher, String... values) throws Exception {
final BasicRestModel[] restModels = Arrays.stream(values).map(s -> new BasicRestModel(s))
.toArray(size -> new BasicRestModel[size]);
return mockMvc.perform(post("/v1/test")
return mockMvc.perform(post("/v1/test/" + "applicationInstanceId")
.contentType(MediaType.APPLICATION_JSON).accept(MediaType.APPLICATION_JSON)
.content(jsonModelList.write(Arrays.asList(restModels)).getJson()))
.andExpect(resultMatcher);
Expand Down
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