Add history table for submission processing (#14)

EBIvariation · Jul 12, 2024 · 821e52d · 821e52d
1 parent 8864295
commit 821e52d
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Showing 6 changed files with 159 additions and 16 deletions.
diff --git a/pom.xml b/pom.xml
@@ -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>

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
@@ -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
@@ -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
@@ -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
@@ -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());
@@ -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<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);

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
@@ -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<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";