saving metadata json (#11)

EBIvariation · May 8, 2024 · 8b1d94f · 8b1d94f
1 parent 6b1b342
commit 8b1d94f
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Showing 8 changed files with 131 additions and 27 deletions.
diff --git a/pom.xml b/pom.xml
@@ -74,6 +74,11 @@
             <artifactId>gson</artifactId>
             <version>2.10.1</version>
         </dependency>
+        <dependency>
+            <groupId>io.hypersistence</groupId>
+            <artifactId>hypersistence-utils-hibernate-55</artifactId>
+            <version>3.7.5</version>
+        </dependency>
     </dependencies>
     <dependencyManagement>
         <dependencies>

diff --git a/src/main/java/uk/ac/ebi/eva/submission/controller/BaseController.java b/src/main/java/uk/ac/ebi/eva/submission/controller/BaseController.java
@@ -39,7 +39,9 @@ public Submission stripUserDetails(Submission submission) {
         Submission responseSubmission = new Submission(submission.getSubmissionId());
         responseSubmission.setStatus(submission.getStatus());
         responseSubmission.setUploadUrl(submission.getUploadUrl());
-
+        responseSubmission.setInitiationTime(submission.getInitiationTime());
+        responseSubmission.setUploadedTime(submission.getUploadedTime());
+        responseSubmission.setCompletionTime(submission.getCompletionTime());
         return responseSubmission;
     }
 }
diff --git a/src/main/java/uk/ac/ebi/eva/submission/controller/submissionws/SubmissionController.java b/src/main/java/uk/ac/ebi/eva/submission/controller/submissionws/SubmissionController.java
@@ -1,5 +1,6 @@
 package uk.ac.ebi.eva.submission.controller.submissionws;
 
+import com.fasterxml.jackson.databind.JsonNode;
 import io.swagger.v3.oas.annotations.Operation;
 import io.swagger.v3.oas.annotations.Parameter;
 import io.swagger.v3.oas.annotations.Parameters;
@@ -10,13 +11,15 @@
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.PostMapping;
 import org.springframework.web.bind.annotation.PutMapping;
+import org.springframework.web.bind.annotation.RequestBody;
 import org.springframework.web.bind.annotation.RequestHeader;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.RestController;
 import uk.ac.ebi.eva.submission.controller.BaseController;
 import uk.ac.ebi.eva.submission.entity.Submission;
 import uk.ac.ebi.eva.submission.entity.SubmissionAccount;
+import uk.ac.ebi.eva.submission.exception.RequiredFieldsMissingException;
 import uk.ac.ebi.eva.submission.model.SubmissionStatus;
 import uk.ac.ebi.eva.submission.service.LsriTokenService;
 import uk.ac.ebi.eva.submission.service.SubmissionService;
@@ -81,15 +84,20 @@ public ResponseEntity<?> initiateSubmission(@RequestHeader("Authorization") Stri
     })
     @PutMapping("submission/{submissionId}/uploaded")
     public ResponseEntity<?> markSubmissionUploaded(@RequestHeader("Authorization") String bearerToken,
-                                                    @PathVariable("submissionId") String submissionId) {
+                                                    @PathVariable("submissionId") String submissionId,
+                                                    @RequestBody JsonNode metadataJson) {
         SubmissionAccount submissionAccount = this.getSubmissionAccount(bearerToken);
         if (Objects.isNull(submissionAccount) || !submissionService.checkUserHasAccessToSubmission(submissionAccount, submissionId)) {
             return new ResponseEntity<>("Unauthorized", HttpStatus.UNAUTHORIZED);
         }
 
-        Submission submission = this.submissionService.markSubmissionUploaded(submissionId);
-        submissionService.sendMailNotificationForStatusUpdate(submissionAccount, submissionId, SubmissionStatus.UPLOADED, true);
-        return new ResponseEntity<>(stripUserDetails(submission), HttpStatus.OK);
+        try {
+            Submission submission = this.submissionService.uploadMetadataJsonAndMarkUploaded(submissionId, metadataJson);
+            submissionService.sendMailNotificationForStatusUpdate(submissionAccount, submissionId, SubmissionStatus.UPLOADED, true);
+            return new ResponseEntity<>(stripUserDetails(submission), HttpStatus.OK);
+        } catch (RequiredFieldsMissingException ex) {
+            return new ResponseEntity<>(ex.getMessage(), HttpStatus.BAD_REQUEST);
+        }
     }
 
     @Operation(summary = "Given a submission id, this endpoint retrieves the current status of a submission")

diff --git a/src/main/java/uk/ac/ebi/eva/submission/entity/SubmissionDetails.java b/src/main/java/uk/ac/ebi/eva/submission/entity/SubmissionDetails.java
@@ -1,5 +1,9 @@
 package uk.ac.ebi.eva.submission.entity;
 
+import com.fasterxml.jackson.databind.JsonNode;
+import io.hypersistence.utils.hibernate.type.json.JsonType;
+import org.hibernate.annotations.TypeDef;
+
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.Id;
@@ -9,8 +13,8 @@
 
 @Entity
 @Table(schema = "eva_submissions", name = "submission_details")
+@TypeDef(typeClass = JsonType.class, defaultForType = JsonNode.class)
 public class SubmissionDetails {
-
     @Id
     @Column(name = "submission_id")
     private String submissionId;
@@ -19,18 +23,20 @@ public class SubmissionDetails {
     @PrimaryKeyJoinColumn(name = "submission_id", referencedColumnName = "submission_id")
     private Submission submission;
 
-    @Column(nullable = false, name = "project_alias")
-    private String projectAlias;
+    @Column(nullable = false, name = "project_title")
+    private String projectTitle;
 
-    @Column(nullable = false, name = "description")
-    private String description;
+    @Column(nullable = false, name = "project_description")
+    private String projectDescription;
 
-    public SubmissionDetails() {
+    @Column(columnDefinition = "jsonb", name = "metadata_json", nullable = false)
+    private JsonNode metadataJson;
 
+    public SubmissionDetails() {
     }
 
-    public SubmissionDetails(Submission submission) {
-        this.submission = submission;
+    public SubmissionDetails(String submissionId) {
+        this.submissionId = submissionId;
     }
 
     public String getSubmissionId() {
@@ -41,19 +47,31 @@ public Submission getSubmission() {
         return submission;
     }
 
-    public String getProjectAlias() {
-        return projectAlias;
+    public void setSubmission(Submission submission) {
+        this.submission = submission;
+    }
+
+    public String getProjectTitle() {
+        return projectTitle;
+    }
+
+    public void setProjectTitle(String projectTitle) {
+        this.projectTitle = projectTitle;
+    }
+
+    public String getProjectDescription() {
+        return projectDescription;
     }
 
-    public void setProjectAlias(String projectAlias) {
-        this.projectAlias = projectAlias;
+    public void setProjectDescription(String projectDescription) {
+        this.projectDescription = projectDescription;
     }
 
-    public String getDescription() {
-        return description;
+    public JsonNode getMetadataJson() {
+        return metadataJson;
     }
 
-    public void setDescription(String description) {
-        this.description = description;
+    public void setMetadataJson(JsonNode metadataJson) {
+        this.metadataJson = metadataJson;
     }
 }
diff --git a/src/main/java/uk/ac/ebi/eva/submission/exception/RequiredFieldsMissingException.java b/src/main/java/uk/ac/ebi/eva/submission/exception/RequiredFieldsMissingException.java
@@ -0,0 +1,7 @@
+package uk.ac.ebi.eva.submission.exception;
+
+public class RequiredFieldsMissingException extends RuntimeException {
+    public RequiredFieldsMissingException(String msg) {
+        super(msg);
+    }
+}
diff --git a/src/main/java/uk/ac/ebi/eva/submission/repository/SubmissionDetailsRepository.java b/src/main/java/uk/ac/ebi/eva/submission/repository/SubmissionDetailsRepository.java
@@ -4,4 +4,5 @@
 import uk.ac.ebi.eva.submission.entity.SubmissionDetails;
 
 public interface SubmissionDetailsRepository extends CrudRepository<SubmissionDetails, String> {
+    SubmissionDetails findBySubmissionId(String submissionId);
 }
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
@@ -1,16 +1,18 @@
 package uk.ac.ebi.eva.submission.service;
 
+import com.fasterxml.jackson.databind.JsonNode;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
 import uk.ac.ebi.eva.submission.entity.Submission;
 import uk.ac.ebi.eva.submission.entity.SubmissionAccount;
+import uk.ac.ebi.eva.submission.entity.SubmissionDetails;
+import uk.ac.ebi.eva.submission.exception.RequiredFieldsMissingException;
 import uk.ac.ebi.eva.submission.exception.SubmissionDoesNotExistException;
 import uk.ac.ebi.eva.submission.model.SubmissionStatus;
 import uk.ac.ebi.eva.submission.repository.SubmissionAccountRepository;
 import uk.ac.ebi.eva.submission.repository.SubmissionDetailsRepository;
 import uk.ac.ebi.eva.submission.repository.SubmissionRepository;
 import uk.ac.ebi.eva.submission.util.EmailNotificationHelper;
-import uk.ac.ebi.eva.submission.util.HTMLHelper;
 import uk.ac.ebi.eva.submission.util.MailSender;
 
 import java.time.LocalDateTime;
@@ -19,6 +21,9 @@
 
 @Service
 public class SubmissionService {
+    private static final String PROJECT = "project";
+    private static final String TITLE = "title";
+    private static final String DESCRIPTION = "description";
 
     private final SubmissionRepository submissionRepository;
 
@@ -68,7 +73,23 @@ public Submission initiateSubmission(SubmissionAccount submissionAccount) {
         return submissionRepository.save(submission);
     }
 
-    public Submission markSubmissionUploaded(String submissionId) {
+    public Submission uploadMetadataJsonAndMarkUploaded(String submissionId, JsonNode metadataJson) {
+        SubmissionDetails submissionDetails = new SubmissionDetails(submissionId);
+        try {
+            JsonNode project = metadataJson.get(PROJECT);
+            String projectTitle = project.get(TITLE).asText();
+            String projectDescription = project.get(DESCRIPTION).asText();
+
+            submissionDetails.setProjectTitle(projectTitle);
+            submissionDetails.setProjectDescription(projectDescription);
+        } catch (Exception e) {
+            throw new RequiredFieldsMissingException("Required fields project title and project description " +
+                    "could not be found in metadata json");
+        }
+
+        submissionDetails.setMetadataJson(metadataJson);
+        submissionDetailsRepository.save(submissionDetails);
+
         Submission submission = submissionRepository.findBySubmissionId(submissionId);
         submission.setStatus(SubmissionStatus.UPLOADED.toString());
         submission.setUploadedTime(LocalDateTime.now());

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
@@ -18,8 +18,10 @@
 import org.testcontainers.junit.jupiter.Testcontainers;
 import uk.ac.ebi.eva.submission.entity.Submission;
 import uk.ac.ebi.eva.submission.entity.SubmissionAccount;
+import uk.ac.ebi.eva.submission.entity.SubmissionDetails;
 import uk.ac.ebi.eva.submission.model.SubmissionStatus;
 import uk.ac.ebi.eva.submission.repository.SubmissionAccountRepository;
+import uk.ac.ebi.eva.submission.repository.SubmissionDetailsRepository;
 import uk.ac.ebi.eva.submission.repository.SubmissionRepository;
 import uk.ac.ebi.eva.submission.service.GlobusDirectoryProvisioner;
 import uk.ac.ebi.eva.submission.service.GlobusTokenRefreshService;
@@ -65,6 +67,9 @@ public class SubmissionWSIntegrationTest {
     @Autowired
     private SubmissionAccountRepository submissionAccountRepository;
 
+    @Autowired
+    private SubmissionDetailsRepository submissionDetailsRepository;
+
     @MockBean
     private WebinTokenService webinTokenService;
 
@@ -230,18 +235,21 @@ public void testSubmissionGetStatus() throws Exception {
 
     @Test
     @Transactional
-    public void testMarkSubmissionUploaded() throws Exception {
+    public void testUploadMetadataJsonAndMarkUploadedd() throws Exception {
         String userToken = "webinUserToken";
         SubmissionAccount submissionAccount = getWebinUserAccount();
         when(webinTokenService.getWebinUserAccountFromToken(anyString())).thenReturn(submissionAccount);
         doNothing().when(mailSender).sendEmail(anyString(), anyString(), anyString());
 
         String submissionId = createNewSubmissionEntry(submissionAccount);
-
+        String projectTitle = "test_project_title";
+        String projectDescription = "test_project_description";
+        String metadataJson = "{\"project\": {\"title\":\"" + projectTitle + "\",\"description\":\"" + projectDescription + "\"}}";
         HttpHeaders httpHeaders = new HttpHeaders();
         httpHeaders.setBearerAuth(userToken);
         mvc.perform(put("/v1/submission/" + submissionId + "/uploaded")
                         .headers(httpHeaders)
+                        .content(metadataJson)
                         .contentType(MediaType.APPLICATION_JSON))
                 .andExpect(status().isOk());
 
@@ -251,6 +259,38 @@ public void testMarkSubmissionUploaded() throws Exception {
         assertThat(submission.getStatus()).isEqualTo(SubmissionStatus.UPLOADED.toString());
         assertThat(submission.getUploadedTime()).isNotNull();
         assertThat(submission.getCompletionTime()).isNull();
+
+        SubmissionDetails submissionDetails = submissionDetailsRepository.findBySubmissionId(submissionId);
+        assertThat(submissionDetails).isNotNull();
+        assertThat(submissionDetails.getSubmissionId()).isEqualTo(submissionId);
+        assertThat(submissionDetails.getProjectTitle()).isEqualTo(projectTitle);
+        assertThat(submissionDetails.getProjectDescription()).isEqualTo(projectDescription);
+        assertThat(submissionDetails.getMetadataJson()).isNotNull();
+        assertThat(submissionDetails.getMetadataJson().get("project").get("title").asText()).isEqualTo(projectTitle);
+        assertThat(submissionDetails.getMetadataJson().get("project").get("title").asText()).isEqualTo(projectTitle);
+    }
+
+    @Test
+    @Transactional
+    public void testRequiredMetadataFieldsNotProvided() throws Exception {
+        String userToken = "webinUserToken";
+        SubmissionAccount submissionAccount = getWebinUserAccount();
+        when(webinTokenService.getWebinUserAccountFromToken(anyString())).thenReturn(submissionAccount);
+        doNothing().when(mailSender).sendEmail(anyString(), anyString(), anyString());
+
+        String submissionId = createNewSubmissionEntry(submissionAccount);
+        String projectDescription = "test_project_description";
+        String metadataJson = "{\"project\": {\"description\":\"" + projectDescription + "\"}}";
+        HttpHeaders httpHeaders = new HttpHeaders();
+        httpHeaders.setBearerAuth(userToken);
+
+        mvc.perform(put("/v1/submission/" + submissionId + "/uploaded")
+                        .headers(httpHeaders)
+                        .content(metadataJson)
+                        .contentType(MediaType.APPLICATION_JSON))
+                .andExpect(status().isBadRequest())
+                .andExpect(content().string("Required fields project title and project description " +
+                        "could not be found in metadata json"));
     }
 
     @Test
@@ -261,11 +301,15 @@ public void testSubmissionDoesNotExistException() throws Exception {
         when(webinTokenService.getWebinUserAccountFromToken(anyString())).thenReturn(submissionAccount);
 
         String submissionId = "wrong_submission_id";
+        String projectTitle = "test_project_title";
+        String projectDescription = "test_project_description";
+        String metadataJson = "{\"project\": {\"title\":\"" + projectTitle + "\",\"description\":\"" + projectDescription + "\"}}";
 
         HttpHeaders httpHeaders = new HttpHeaders();
         httpHeaders.setBearerAuth(userToken);
         mvc.perform(put("/v1/submission/" + submissionId + "/uploaded")
                         .headers(httpHeaders)
+                        .content(metadataJson)
                         .contentType(MediaType.APPLICATION_JSON))
                 .andExpect(status().isNotFound())
                 .andExpect(content().string("Given submission with id " + submissionId + " does not exist"));
@@ -274,7 +318,6 @@ public void testSubmissionDoesNotExistException() throws Exception {
     @Test
     @Transactional
     public void testMarkSubmissionStatusCorrect() throws Exception {
-        String userToken = "webinUserToken";
         SubmissionAccount submissionAccount = getWebinUserAccount();
         when(webinTokenService.getWebinUserAccountFromToken(anyString())).thenReturn(submissionAccount);
 
@@ -298,7 +341,6 @@ public void testMarkSubmissionStatusCorrect() throws Exception {
     @Test
     @Transactional
     public void testMarkSubmissionStatusWrong() throws Exception {
-        String userToken = "webinUserToken";
         SubmissionAccount submissionAccount = getWebinUserAccount();
         when(webinTokenService.getWebinUserAccountFromToken(anyString())).thenReturn(submissionAccount);