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EVA-3470 Add audit/history table for submission processing #14

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merged 1 commit into from
Jul 12, 2024
Merged

EVA-3470 Add audit/history table for submission processing #14

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4 changes: 4 additions & 0 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,10 @@
<artifactId>hypersistence-utils-hibernate-55</artifactId>
<version>3.7.5</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-envers</artifactId>
</dependency>
</dependencies>
<dependencyManagement>
<dependencies>
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16 changes: 12 additions & 4 deletions src/main/java/uk/ac/ebi/eva/submission/controller/admin/AdminController.java
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Expand Up @@ -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")
Expand Down Expand Up @@ -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")
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4 changes: 4 additions & 0 deletions src/main/java/uk/ac/ebi/eva/submission/entity/SubmissionProcessing.java
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@@ -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;
Expand All @@ -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 {

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10 changes: 4 additions & 6 deletions src/main/java/uk/ac/ebi/eva/submission/exception/SubmissionDoesNotExistException.java
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@@ -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");
}
}
16 changes: 14 additions & 2 deletions src/main/java/uk/ac/ebi/eva/submission/service/SubmissionService.java
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Expand Up @@ -109,14 +109,17 @@ 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();
}

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

Expand All @@ -156,7 +159,16 @@ public List<SubmissionProcessing> getSubmissionsByProcessingStepAndStatus(Submis
public SubmissionProcessing markSubmissionProcessStepAndStatus(String submissionId,
SubmissionProcessingStep step,
SubmissionProcessingStatus status) {
Optional<Submission> 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);
Expand Down
125 changes: 121 additions & 4 deletions src/test/java/uk/ac/ebi/eva/submission/integration/SubmissionWSIntegrationTest.java
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@@ -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;
Expand Down Expand Up @@ -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;
Expand All @@ -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
Expand All @@ -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;

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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 {
Expand Down Expand Up @@ -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<Number> 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";
Expand Down
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