Merge pull request #13 from tcezard/EVA3533_processing_status

EVA-3533 Endpoints to retrieve and mark submission processing status

src/main/java/uk/ac/ebi/eva/submission/controller/BaseController.java

@@ -9,7 +9,9 @@
 import uk.ac.ebi.eva.submission.service.LsriTokenService;
 import uk.ac.ebi.eva.submission.service.WebinTokenService;
 
+import java.util.List;
 import java.util.Objects;
+import java.util.stream.Collectors;
 
 public class BaseController {
     private final WebinTokenService webinTokenService;
@@ -35,6 +37,10 @@ public SubmissionAccount getSubmissionAccount(String bearerToken) {
         return submissionAccount;
     }
 
+    public List<Submission> stripUserDetails(List<Submission> submissions){
+        return submissions.stream().map(this::stripUserDetails).collect(Collectors.toList());
+    }
+
     public Submission stripUserDetails(Submission submission) {
         Submission responseSubmission = new Submission(submission.getSubmissionId());
         responseSubmission.setStatus(submission.getStatus());

src/main/java/uk/ac/ebi/eva/submission/controller/admin/AdminController.java

@@ -7,17 +7,24 @@
 import io.swagger.v3.oas.annotations.security.SecurityRequirement;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.PutMapping;
 import org.springframework.web.bind.annotation.RequestMapping;
 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.SubmissionProcessing;
+import uk.ac.ebi.eva.submission.exception.SubmissionDoesNotExistException;
+import uk.ac.ebi.eva.submission.model.SubmissionProcessingStatus;
+import uk.ac.ebi.eva.submission.model.SubmissionProcessingStep;
 import uk.ac.ebi.eva.submission.model.SubmissionStatus;
 import uk.ac.ebi.eva.submission.service.LsriTokenService;
 import uk.ac.ebi.eva.submission.service.SubmissionService;
 import uk.ac.ebi.eva.submission.service.WebinTokenService;
 
+import java.util.List;
+
 @RestController
 @RequestMapping("/v1/admin")
 public class AdminController extends BaseController {
@@ -44,4 +51,50 @@ public ResponseEntity<?> markSubmissionStatus(@PathVariable("submissionId") Stri
         Submission submission = this.submissionService.markSubmissionStatus(submissionId, status);
         return new ResponseEntity<>(stripUserDetails(submission), HttpStatus.OK);
     }
+
+    @Operation(summary = "This endpoint retrieves all the submissions of a specific status present in the database")
+    @Parameters({
+            @Parameter(name="status", description = "Desired status of the submission ",
+                    required = true, in= ParameterIn.PATH)
+    })
+    @GetMapping("submissions/status/{status}")
+    public ResponseEntity<?> getSubmissionsbyStatus(@PathVariable("status") SubmissionStatus status) {
+        List<Submission> submissions = submissionService.getSubmissionsByStatus(status);
+        return new ResponseEntity<>(stripUserDetails(submissions), HttpStatus.OK);
+    }
+
+    @Operation(summary = "Given a submission id, this endpoint updates the processing status of the submission to the one provided",
+            security = {@SecurityRequirement(name = "basicAuth")
+    })
+    @Parameters({
+            @Parameter(name="submissionId", description = "Id of the submission whose status needs to be updated",
+                    required = true, in= ParameterIn.PATH),
+            @Parameter(name="step", description = "The processing step of the submission",
+                    required = true, in= ParameterIn.PATH),
+            @Parameter(name="status", description = "The status of the processing step for this submission",
+                    required = true, in= ParameterIn.PATH)
+    })
+    @PutMapping("submission-process/{submissionId}/{step}/{status}")
+    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);
+    }
+
+    @Operation(summary = "This endpoint retrieves all the submissions from the database with given step and status")
+    @Parameters({
+            @Parameter(name="step", description = "The processing step of the submission.",
+                    required = true, in= ParameterIn.PATH),
+            @Parameter(name="status", description = "The status of the submission processing step.",
+                    required = true, in= ParameterIn.PATH)
+    })
+    @GetMapping("submission-processes/{step}/{status}")
+    public ResponseEntity<?> getSubmissionsProcessingByStepAndStatus(
+            @PathVariable("step") SubmissionProcessingStep step,
+            @PathVariable("status") SubmissionProcessingStatus status) {
+        List<SubmissionProcessing> submissions = submissionService.getSubmissionsByProcessingStepAndStatus(step, status);
+        return new ResponseEntity<>(submissions, HttpStatus.OK);
+    }
+
 }

src/main/java/uk/ac/ebi/eva/submission/entity/SubmissionProcessing.java

@@ -0,0 +1,110 @@
+package uk.ac.ebi.eva.submission.entity;
+
+import org.hibernate.annotations.UpdateTimestamp;
+import org.springframework.lang.NonNull;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.OneToOne;
+import javax.persistence.Table;
+import java.time.LocalDateTime;
+import java.util.Objects;
+
+@Entity
+@Table(schema = "eva_submissions", name = "submission_processing_status")
+public class SubmissionProcessing {
+
+    public SubmissionProcessing() {
+
+    }
+
+    public SubmissionProcessing(String submissionId) {
+        this.submissionId = submissionId;
+    }
+
+    @Id
+    @NonNull
+    @Column(nullable = false, name = "submission_id")
+    private String submissionId;
+
+    @OneToOne
+    @JoinColumn(name = "submission_id", referencedColumnName = "submission_id", insertable = false, updatable = false)
+    private Submission submission;
+
+    @NonNull
+    @Column(nullable = false)
+    private String step;
+
+    @NonNull
+    @Column(nullable = false)
+    private String status;
+
+    @NonNull
+    @Column(nullable = false, columnDefinition = "INTEGER DEFAULT 5")
+    private Integer priority = 5;
+
+    @Column(nullable = false)
+    @UpdateTimestamp
+    private LocalDateTime lastUpdateTime;
+
+    public String getSubmissionId() {
+        return submissionId;
+    }
+
+    @NonNull
+    public String getStep() {
+        return step;
+    }
+
+    public void setStep(@NonNull String step) {
+        this.step = step;
+    }
+
+    @NonNull
+    public String getStatus() {
+        return status;
+    }
+
+    public void setStatus(@NonNull String status) {
+        this.status = status;
+    }
+
+    @NonNull
+    public Integer getPriority() {
+        return priority;
+    }
+
+    public void setPriority(@NonNull Integer priority) {
+        this.priority = priority;
+    }
+
+    public LocalDateTime getLastUpdateTime() {
+        return lastUpdateTime;
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (!(o instanceof SubmissionProcessing)) return false;
+        SubmissionProcessing that = (SubmissionProcessing) o;
+        return getSubmissionId().equals(that.getSubmissionId());
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(getSubmissionId());
+    }
+
+    @Override
+    public String toString() {
+        return "Submission{" +
+                "submissionId='" + submissionId + '\'' +
+                ", step=" + step +
+                ", status=" + status +
+                ", priority=" + priority +
+                ", lastUpdateTime=" + lastUpdateTime +
+                '}';
+    }
+}

src/main/java/uk/ac/ebi/eva/submission/model/SubmissionProcessingStatus.java

@@ -0,0 +1,5 @@
+package uk.ac.ebi.eva.submission.model;
+
+public enum SubmissionProcessingStatus {
+    READY_FOR_PROCESSING, FAILURE,  SUCCESS, RUNNING, ON_HOLD
+}

src/main/java/uk/ac/ebi/eva/submission/model/SubmissionProcessingStep.java

@@ -0,0 +1,5 @@
+package uk.ac.ebi.eva.submission.model;
+
+public enum SubmissionProcessingStep {
+    INGESTION, VALIDATION, BROKERING,
+}

src/main/java/uk/ac/ebi/eva/submission/model/SubmissionStatus.java

@@ -1,6 +1,6 @@
 package uk.ac.ebi.eva.submission.model;
 
 public enum SubmissionStatus {
-    OPEN, UPLOADED, COMPLETED, TIMEOUT, FAILED, CANCELLED
+    OPEN, UPLOADED, COMPLETED, TIMEOUT, FAILED, CANCELLED, PROCESSING
 
 }

src/main/java/uk/ac/ebi/eva/submission/repository/SubmissionProcessingRepository.java

@@ -0,0 +1,13 @@
+package uk.ac.ebi.eva.submission.repository;
+
+import org.springframework.data.repository.CrudRepository;
+import uk.ac.ebi.eva.submission.entity.SubmissionProcessing;
+
+import java.util.List;
+
+public interface SubmissionProcessingRepository extends CrudRepository<SubmissionProcessing, String> {
+
+    SubmissionProcessing findBySubmissionId(String submissionId);
+
+    List<SubmissionProcessing> findByStepAndStatus(String step, String status);
+}

src/main/java/uk/ac/ebi/eva/submission/repository/SubmissionRepository.java

@@ -3,6 +3,10 @@
 import org.springframework.data.repository.CrudRepository;
 import uk.ac.ebi.eva.submission.entity.Submission;
 
+import java.util.List;
+
 public interface SubmissionRepository extends CrudRepository<Submission, String> {
     Submission findBySubmissionId(String submissionId);
+
+    List<Submission> findByStatus(String status);
 }

src/main/java/uk/ac/ebi/eva/submission/service/SubmissionService.java

@@ -6,16 +6,21 @@
 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.entity.SubmissionProcessing;
 import uk.ac.ebi.eva.submission.exception.RequiredFieldsMissingException;
 import uk.ac.ebi.eva.submission.exception.SubmissionDoesNotExistException;
+import uk.ac.ebi.eva.submission.model.SubmissionProcessingStatus;
+import uk.ac.ebi.eva.submission.model.SubmissionProcessingStep;
 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.SubmissionProcessingRepository;
 import uk.ac.ebi.eva.submission.repository.SubmissionRepository;
 import uk.ac.ebi.eva.submission.util.EmailNotificationHelper;
 import uk.ac.ebi.eva.submission.util.MailSender;
 
 import java.time.LocalDateTime;
+import java.util.List;
 import java.util.Optional;
 import java.util.UUID;
 
@@ -31,6 +36,8 @@ public class SubmissionService {
 
     private final SubmissionDetailsRepository submissionDetailsRepository;
 
+    private final SubmissionProcessingRepository submissionProcessingRepository;
+
     private final GlobusDirectoryProvisioner globusDirectoryProvisioner;
 
     private final MailSender mailSender;
@@ -43,11 +50,13 @@ public class SubmissionService {
     public SubmissionService(SubmissionRepository submissionRepository,
                              SubmissionAccountRepository submissionAccountRepository,
                              SubmissionDetailsRepository submissionDetailsRepository,
+                             SubmissionProcessingRepository submissionProcessingRepository,
                              GlobusDirectoryProvisioner globusDirectoryProvisioner,
                              MailSender mailSender, EmailNotificationHelper emailHelper) {
         this.submissionRepository = submissionRepository;
         this.submissionAccountRepository = submissionAccountRepository;
         this.submissionDetailsRepository = submissionDetailsRepository;
+        this.submissionProcessingRepository = submissionProcessingRepository;
         this.globusDirectoryProvisioner = globusDirectoryProvisioner;
         this.mailSender = mailSender;
         this.emailHelper = emailHelper;
@@ -133,4 +142,25 @@ public void sendMailNotificationForStatusUpdate(SubmissionAccount submissionAcco
         String body = emailHelper.getTextForSubmissionStatusUpdate(submissionAccount, submissionId, submissionStatus, success);
         mailSender.sendEmail(sendTo, subject, body);
     }
+
+    public List<Submission> getSubmissionsByStatus(SubmissionStatus status) {
+        return submissionRepository.findByStatus(status.toString());
+    }
+
+    public List<SubmissionProcessing> getSubmissionsByProcessingStepAndStatus(SubmissionProcessingStep step,
+                                                                              SubmissionProcessingStatus status) {
+        return submissionProcessingRepository.findByStepAndStatus(step.toString(), status.toString());
+
+    }
+
+    public SubmissionProcessing markSubmissionProcessStepAndStatus(String submissionId,
+                                                                   SubmissionProcessingStep step,
+                                                                   SubmissionProcessingStatus status) {
+        SubmissionProcessing submissionProc = submissionProcessingRepository.findBySubmissionId(submissionId);
+        submissionProc.setStep(step.toString());
+        submissionProc.setStatus(status.toString());
+        return submissionProcessingRepository.save(submissionProc);
+    }
+
+
 }