diff --git a/pom.xml b/pom.xml
index bc06050..d8425b3 100644
--- a/pom.xml
+++ b/pom.xml
@@ -79,6 +79,10 @@
hypersistence-utils-hibernate-55
3.7.5
+
+ org.hibernate
+ hibernate-envers
+
diff --git a/src/main/java/uk/ac/ebi/eva/submission/controller/admin/AdminController.java b/src/main/java/uk/ac/ebi/eva/submission/controller/admin/AdminController.java
index e91a464..0b69e9a 100644
--- a/src/main/java/uk/ac/ebi/eva/submission/controller/admin/AdminController.java
+++ b/src/main/java/uk/ac/ebi/eva/submission/controller/admin/AdminController.java
@@ -48,8 +48,12 @@ public AdminController(SubmissionService submissionService, WebinTokenService we
@PutMapping("submission/{submissionId}/status/{status}")
public ResponseEntity markSubmissionStatus(@PathVariable("submissionId") String submissionId,
@PathVariable("status") SubmissionStatus status) {
- Submission submission = this.submissionService.markSubmissionStatus(submissionId, status);
- return new ResponseEntity<>(stripUserDetails(submission), HttpStatus.OK);
+ try {
+ Submission submission = this.submissionService.markSubmissionStatus(submissionId, status);
+ return new ResponseEntity<>(stripUserDetails(submission), HttpStatus.OK);
+ } catch (SubmissionDoesNotExistException ex) {
+ return new ResponseEntity<>(ex.getMessage(), HttpStatus.NOT_FOUND);
+ }
}
@Operation(summary = "This endpoint retrieves all the submissions of a specific status present in the database")
@@ -78,8 +82,12 @@ public ResponseEntity getSubmissionsbyStatus(@PathVariable("status") Submissi
public ResponseEntity markSubmissionProcessStepAndStatus(@PathVariable("submissionId") String submissionId,
@PathVariable("step") SubmissionProcessingStep step,
@PathVariable("status") SubmissionProcessingStatus status) {
- SubmissionProcessing submissionProc = this.submissionService.markSubmissionProcessStepAndStatus(submissionId, step, status);
- return new ResponseEntity<>(submissionProc, HttpStatus.OK);
+ try {
+ SubmissionProcessing submissionProc = this.submissionService.markSubmissionProcessStepAndStatus(submissionId, step, status);
+ return new ResponseEntity<>(submissionProc, HttpStatus.OK);
+ } catch (SubmissionDoesNotExistException ex) {
+ return new ResponseEntity<>(ex.getMessage(), HttpStatus.NOT_FOUND);
+ }
}
@Operation(summary = "This endpoint retrieves all the submissions from the database with given step and status")
diff --git a/src/main/java/uk/ac/ebi/eva/submission/entity/SubmissionProcessing.java b/src/main/java/uk/ac/ebi/eva/submission/entity/SubmissionProcessing.java
index 4aa6378..52db166 100644
--- a/src/main/java/uk/ac/ebi/eva/submission/entity/SubmissionProcessing.java
+++ b/src/main/java/uk/ac/ebi/eva/submission/entity/SubmissionProcessing.java
@@ -1,6 +1,7 @@
package uk.ac.ebi.eva.submission.entity;
import org.hibernate.annotations.UpdateTimestamp;
+import org.hibernate.envers.Audited;
import org.springframework.lang.NonNull;
import javax.persistence.Column;
@@ -12,7 +13,10 @@
import java.time.LocalDateTime;
import java.util.Objects;
+import static org.hibernate.envers.RelationTargetAuditMode.NOT_AUDITED;
+
@Entity
+@Audited(targetAuditMode = NOT_AUDITED)
@Table(schema = "eva_submissions", name = "submission_processing_status")
public class SubmissionProcessing {
diff --git a/src/main/java/uk/ac/ebi/eva/submission/exception/SubmissionDoesNotExistException.java b/src/main/java/uk/ac/ebi/eva/submission/exception/SubmissionDoesNotExistException.java
index 9f2f6fc..52dfad8 100644
--- a/src/main/java/uk/ac/ebi/eva/submission/exception/SubmissionDoesNotExistException.java
+++ b/src/main/java/uk/ac/ebi/eva/submission/exception/SubmissionDoesNotExistException.java
@@ -1,10 +1,8 @@
package uk.ac.ebi.eva.submission.exception;
-public class SubmissionDoesNotExistException extends RuntimeException{
- public SubmissionDoesNotExistException(){
- super("Submission does not exist");
- }
- public SubmissionDoesNotExistException(String msg){
- super(msg);
+public class SubmissionDoesNotExistException extends RuntimeException {
+
+ public SubmissionDoesNotExistException(String submissionId) {
+ super("Submission with id " + submissionId + " does not exist");
}
}
diff --git a/src/main/java/uk/ac/ebi/eva/submission/service/SubmissionService.java b/src/main/java/uk/ac/ebi/eva/submission/service/SubmissionService.java
index b87427e..cdc0152 100644
--- a/src/main/java/uk/ac/ebi/eva/submission/service/SubmissionService.java
+++ b/src/main/java/uk/ac/ebi/eva/submission/service/SubmissionService.java
@@ -109,7 +109,7 @@ public Submission uploadMetadataJsonAndMarkUploaded(String submissionId, JsonNod
public String getSubmissionStatus(String submissionId) {
Submission submission = submissionRepository.findBySubmissionId(submissionId);
if (submission == null) {
- throw new SubmissionDoesNotExistException("Submission with Id " + submissionId + " does not exist");
+ throw new SubmissionDoesNotExistException(submissionId);
}
return submission.getStatus();
@@ -117,6 +117,9 @@ public String getSubmissionStatus(String submissionId) {
public Submission markSubmissionStatus(String submissionId, SubmissionStatus status) {
Submission submission = submissionRepository.findBySubmissionId(submissionId);
+ if (submission == null) {
+ throw new SubmissionDoesNotExistException(submissionId);
+ }
submission.setStatus(status.toString());
if (status == SubmissionStatus.COMPLETED) {
submission.setCompletionTime(LocalDateTime.now());
@@ -131,7 +134,7 @@ public boolean checkUserHasAccessToSubmission(SubmissionAccount account, String
SubmissionAccount submissionAccount = optSubmission.get().getSubmissionAccount();
return submissionAccount.getId().equals(account.getId());
} else {
- throw new SubmissionDoesNotExistException("Given submission with id " + submissionId + " does not exist");
+ throw new SubmissionDoesNotExistException(submissionId);
}
}
@@ -156,7 +159,16 @@ public List getSubmissionsByProcessingStepAndStatus(Submis
public SubmissionProcessing markSubmissionProcessStepAndStatus(String submissionId,
SubmissionProcessingStep step,
SubmissionProcessingStatus status) {
+ Optional submission = submissionRepository.findById(submissionId);
+ if (!submission.isPresent()) {
+ throw new SubmissionDoesNotExistException(submissionId);
+ }
+
SubmissionProcessing submissionProc = submissionProcessingRepository.findBySubmissionId(submissionId);
+ if (submissionProc == null) {
+ submissionProc = new SubmissionProcessing(submissionId);
+ }
+
submissionProc.setStep(step.toString());
submissionProc.setStatus(status.toString());
return submissionProcessingRepository.save(submissionProc);
diff --git a/src/test/java/uk/ac/ebi/eva/submission/integration/SubmissionWSIntegrationTest.java b/src/test/java/uk/ac/ebi/eva/submission/integration/SubmissionWSIntegrationTest.java
index e3f2154..7aed856 100644
--- a/src/test/java/uk/ac/ebi/eva/submission/integration/SubmissionWSIntegrationTest.java
+++ b/src/test/java/uk/ac/ebi/eva/submission/integration/SubmissionWSIntegrationTest.java
@@ -1,7 +1,9 @@
package uk.ac.ebi.eva.submission.integration;
import com.fasterxml.jackson.databind.ObjectMapper;
-import org.jetbrains.annotations.NotNull;
+import org.hibernate.envers.AuditReader;
+import org.hibernate.envers.AuditReaderFactory;
+import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
@@ -35,6 +37,7 @@
import uk.ac.ebi.eva.submission.service.WebinTokenService;
import uk.ac.ebi.eva.submission.util.MailSender;
+import javax.persistence.EntityManager;
import java.time.LocalDateTime;
import java.util.ArrayList;
import java.util.HashSet;
@@ -51,7 +54,9 @@
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.put;
-import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.content;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath;
+import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
@SpringBootTest
@AutoConfigureMockMvc
@@ -64,6 +69,9 @@ public class SubmissionWSIntegrationTest {
@Value("${controller.auth.admin.password}")
private String TEST_ADMIN_PASSWORD;
+ @Autowired
+ private EntityManager entityManager;
+
@Autowired
private MockMvc mvc;
@@ -253,7 +261,7 @@ public void testSubmissionGetStatusSubmissionDoesNotExist() throws Exception {
mvc.perform(get("/v1/submission/" + submissionId + "/status")
.headers(httpHeaders)
.contentType(MediaType.APPLICATION_JSON))
- .andExpectAll(status().isNotFound(), content().string("Submission with Id test123 does not exist"));
+ .andExpectAll(status().isNotFound(), content().string("Submission with id " + submissionId + " does not exist"));
}
@Test
@@ -335,7 +343,7 @@ public void testSubmissionDoesNotExistException() throws Exception {
.content(metadataJson)
.contentType(MediaType.APPLICATION_JSON))
.andExpect(status().isNotFound())
- .andExpect(content().string("Given submission with id " + submissionId + " does not exist"));
+ .andExpect(content().string("Submission with id " + submissionId + " does not exist"));
}
@Test
@@ -377,6 +385,23 @@ public void testMarkSubmissionStatusWrong() throws Exception {
.andExpect(status().isBadRequest());
}
+ @Test
+ @Transactional
+ public void testMarkSubmissionStatusSubmissionDoesNotExist() throws Exception {
+ SubmissionAccount submissionAccount = getWebinUserAccount();
+ when(webinTokenService.getWebinUserAccountFromToken(anyString())).thenReturn(submissionAccount);
+
+ String submissionId = "test-wrong-submission-id";
+
+ HttpHeaders httpHeaders = new HttpHeaders();
+ httpHeaders.setBasicAuth(TEST_ADMIN_USERNAME, TEST_ADMIN_PASSWORD);
+ mvc.perform(put("/v1/admin/submission/" + submissionId + "/status/COMPLETED")
+ .headers(httpHeaders)
+ .contentType(MediaType.APPLICATION_JSON))
+ .andExpect(status().isNotFound())
+ .andExpect(content().string("Submission with id " + submissionId + " does not exist"));
+ }
+
@Test
@Transactional
public void testGetSubmissionByStatus() throws Exception {
@@ -449,6 +474,98 @@ public void testMarkSubmissionProcessStepAndStatus() throws Exception {
assertThat(submissionProc.getLastUpdateTime()).isNotNull();
}
+ @Test
+ @Transactional
+ public void testMarkSubmissionProcessStepAndStatusCreateFirstEntry() throws Exception {
+ SubmissionAccount submissionAccount = getWebinUserAccount();
+ when(webinTokenService.getWebinUserAccountFromToken(anyString())).thenReturn(submissionAccount);
+
+ String submissionId = createNewSubmissionEntry(submissionAccount, SubmissionStatus.PROCESSING);
+
+ HttpHeaders httpHeaders = new HttpHeaders();
+ httpHeaders.setBasicAuth(TEST_ADMIN_USERNAME, TEST_ADMIN_PASSWORD);
+ mvc.perform(put("/v1/admin/submission-process/" + submissionId + "/" + SubmissionProcessingStep.VALIDATION + "/" + SubmissionProcessingStatus.SUCCESS)
+ .headers(httpHeaders)
+ .contentType(MediaType.APPLICATION_JSON))
+ .andExpect(status().isOk());
+
+ SubmissionProcessing submissionProc = submissionProcessingRepository.findBySubmissionId(submissionId);
+ assertThat(submissionProc).isNotNull();
+ assertThat(submissionProc.getSubmissionId()).isEqualTo(submissionId);
+ assertThat(submissionProc.getStep()).isEqualTo(SubmissionProcessingStep.VALIDATION.toString());
+ assertThat(submissionProc.getStatus()).isEqualTo(SubmissionProcessingStatus.SUCCESS.toString());
+ assertThat(submissionProc.getLastUpdateTime()).isNotNull();
+ }
+
+ @Test
+ @Transactional
+ public void testMarkSubmissionProcessStepAndStatusSubmissionDoesNotExist() throws Exception {
+ SubmissionAccount submissionAccount = getWebinUserAccount();
+ when(webinTokenService.getWebinUserAccountFromToken(anyString())).thenReturn(submissionAccount);
+
+ String submissionId = "test-wrong-submission-id";
+
+ HttpHeaders httpHeaders = new HttpHeaders();
+ httpHeaders.setBasicAuth(TEST_ADMIN_USERNAME, TEST_ADMIN_PASSWORD);
+ mvc.perform(put("/v1/admin/submission-process/" + submissionId + "/" + SubmissionProcessingStep.VALIDATION + "/" + SubmissionProcessingStatus.SUCCESS)
+ .headers(httpHeaders)
+ .contentType(MediaType.APPLICATION_JSON))
+ .andExpect(status().isNotFound())
+ .andExpect(content().string("Submission with id " + submissionId + " does not exist"));
+ }
+
+
+ @Disabled
+ @Test
+ @Transactional
+ public void testSubmissionProcessingHistory() throws Exception {
+ SubmissionAccount submissionAccount = getWebinUserAccount();
+ when(webinTokenService.getWebinUserAccountFromToken(anyString())).thenReturn(submissionAccount);
+
+ String submissionId = createNewSubmissionEntry(submissionAccount, SubmissionStatus.PROCESSING);
+
+ HttpHeaders httpHeaders = new HttpHeaders();
+ httpHeaders.setBasicAuth(TEST_ADMIN_USERNAME, TEST_ADMIN_PASSWORD);
+ mvc.perform(put("/v1/admin/submission-process/" + submissionId + "/" + SubmissionProcessingStep.VALIDATION + "/" + SubmissionProcessingStatus.READY_FOR_PROCESSING)
+ .headers(httpHeaders)
+ .contentType(MediaType.APPLICATION_JSON))
+ .andExpect(status().isOk());
+
+ SubmissionProcessing submissionProc = submissionProcessingRepository.findBySubmissionId(submissionId);
+ assertThat(submissionProc.getSubmissionId()).isEqualTo(submissionId);
+ assertThat(submissionProc.getStep()).isEqualTo(SubmissionProcessingStep.VALIDATION.toString());
+ assertThat(submissionProc.getStatus()).isEqualTo(SubmissionProcessingStatus.READY_FOR_PROCESSING.toString());
+
+ mvc.perform(put("/v1/admin/submission-process/" + submissionId + "/" + SubmissionProcessingStep.VALIDATION + "/" + SubmissionProcessingStatus.FAILURE)
+ .headers(httpHeaders)
+ .contentType(MediaType.APPLICATION_JSON))
+ .andExpect(status().isOk());
+
+ submissionProc = submissionProcessingRepository.findBySubmissionId(submissionId);
+ assertThat(submissionProc.getSubmissionId()).isEqualTo(submissionId);
+ assertThat(submissionProc.getStep()).isEqualTo(SubmissionProcessingStep.VALIDATION.toString());
+ assertThat(submissionProc.getStatus()).isEqualTo(SubmissionProcessingStatus.FAILURE.toString());
+
+ // Assert Submission Processing History Entry inserted successfully
+ AuditReader auditReader = AuditReaderFactory.get(entityManager);
+ List revisions = auditReader.getRevisions(SubmissionProcessing.class, submissionId);
+ assertThat(revisions).isNotEmpty();
+
+ Number firstRevision = revisions.get(0);
+ SubmissionProcessing auditEntryFirstRev = auditReader.find(SubmissionProcessing.class, submissionId, firstRevision);
+ assertThat(auditEntryFirstRev).isNotNull();
+ assertThat(auditEntryFirstRev.getSubmissionId()).isEqualTo(submissionId);
+ assertThat(auditEntryFirstRev.getStep()).isEqualTo(SubmissionProcessingStep.VALIDATION.toString());
+ assertThat(auditEntryFirstRev.getStatus()).isEqualTo(SubmissionProcessingStatus.READY_FOR_PROCESSING.toString());
+
+ Number secondRevision = revisions.get(1);
+ SubmissionProcessing auditEntrySecondRev = auditReader.find(SubmissionProcessing.class, submissionId, secondRevision);
+ assertThat(auditEntrySecondRev).isNotNull();
+ assertThat(auditEntrySecondRev.getSubmissionId()).isEqualTo(submissionId);
+ assertThat(auditEntrySecondRev.getStep()).isEqualTo(SubmissionProcessingStep.VALIDATION.toString());
+ assertThat(auditEntrySecondRev.getStatus()).isEqualTo(SubmissionProcessingStatus.FAILURE.toString());
+ }
+
private SubmissionAccount getWebinUserAccount() {
String accountId = "webinAccountId";