Merge pull request #16 from EBISPOT/develop

Author: tudorgroza

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>uk.ac.ebi.spot.gwasdepo</groupId>
     <artifactId>gwasdepo-ingest-service</artifactId>
-    <version>0.0.6</version>
+    <version>0.0.7</version>
     <packaging>jar</packaging>
 
     <name>GWAS Deposition App Ingest Service</name>
@@ -66,7 +66,7 @@
         <dependency>
             <groupId>uk.ac.ebi.spot.gwasdepo</groupId>
             <artifactId>gwasdepo-commons</artifactId>
-            <version>1.0.12</version>
+            <version>1.0.13</version>
         </dependency>
 
         <dependency>

src/main/java/uk/ac/ebi/spot/gwas/deposition/ingest/repository/SubmissionRepository.java

@@ -14,5 +14,7 @@ public interface SubmissionRepository extends MongoRepository<Submission, String
 
     List<Submission> findByArchived(boolean archived);
 
+    List<Submission> findByOverallStatusAndArchived(String status, boolean archived);
+
     List<Submission> findByBodyOfWorksContainsAndArchived(String bowId, boolean archived);
 }

src/main/java/uk/ac/ebi/spot/gwas/deposition/ingest/rest/controllers/EnvelopeSubmissionsController.java

@@ -37,7 +37,7 @@ public class EnvelopeSubmissionsController {
     @ResponseStatus(HttpStatus.OK)
     public List<SubmissionEnvelopeDto> getSubmissions() {
         log.info("Request to retrieve all submissions.");
-        List<Submission> submissions = submissionService.getSubmissions(null);
+        List<Submission> submissions = submissionService.getSubmissions(null, null);
         log.info("Found {} submissions.", submissions.size());
         List<SubmissionEnvelopeDto> submissionDtos = submissionAssemblyService.assembleEnvelopes(submissions);
         return submissionDtos;

src/main/java/uk/ac/ebi/spot/gwas/deposition/ingest/rest/controllers/SubmissionsController.java

@@ -52,8 +52,10 @@ public SubmissionDto getSubmission(@PathVariable String submissionId) {
     @GetMapping(produces = MediaType.APPLICATION_JSON_VALUE)
     @ResponseStatus(HttpStatus.OK)
     public List<SubmissionDto> getSubmissions(@RequestParam(value = IngestServiceConstants.PARAM_PMID, required = false)
-                                                      String pmid) {
-        log.info("Request to retrieve all submissions - including for PMID: {}", pmid);
+                                                      String pmid,
+                                              @RequestParam(value = IngestServiceConstants.PARAM_STATUS, required = false)
+                                                      String status) {
+        log.info("Request to retrieve all submissions - including for PMID: {} | {}", pmid, status);
         String pubId = null;
         if (pmid != null) {
             try {
@@ -65,7 +67,7 @@ public List<SubmissionDto> getSubmissions(@RequestParam(value = IngestServiceCon
             }
         }
 
-        List<Submission> submissions = submissionService.getSubmissions(pubId);
+        List<Submission> submissions = submissionService.getSubmissions(pubId, status);
         log.info("Found {} submissions.", submissions.size());
         List<SubmissionDto> submissionDtos = new ArrayList<>();
         for (Submission submission : submissions) {

src/main/java/uk/ac/ebi/spot/gwas/deposition/ingest/service/SubmissionService.java

@@ -8,7 +8,7 @@ public interface SubmissionService {
 
     Submission getSubmission(String submissionId);
 
-    List<Submission> getSubmissions(String publicationId);
+    List<Submission> getSubmissions(String publicationId, String status);
 
     Submission updateSubmission(String submissionId, String status);
 

src/main/java/uk/ac/ebi/spot/gwas/deposition/ingest/service/impl/SubmissionServiceImpl.java

@@ -17,6 +17,7 @@
 import uk.ac.ebi.spot.gwas.deposition.ingest.repository.SubmissionRepository;
 import uk.ac.ebi.spot.gwas.deposition.ingest.repository.UserRepository;
 import uk.ac.ebi.spot.gwas.deposition.ingest.service.SubmissionService;
+import uk.ac.ebi.spot.gwas.deposition.ingest.util.SubmissionsUtil;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -53,16 +54,30 @@ public Submission getSubmission(String submissionId) {
     }
 
     @Override
-    public List<Submission> getSubmissions(String publicationId) {
-        log.info("Retrieving submissions.");
+    public List<Submission> getSubmissions(String publicationId, String status) {
+        log.info("Retrieving submissions: {} | {}", publicationId, status);
         if (publicationId != null) {
             Optional<Submission> optionalSubmission = submissionRepository.findByPublicationIdAndArchived(publicationId, false);
             if (optionalSubmission.isPresent()) {
-                return Arrays.asList(new Submission[] {optionalSubmission.get()});
+                return Arrays.asList(new Submission[]{optionalSubmission.get()});
             }
             return new ArrayList<>();
         }
-        List<Submission> submissions = submissionRepository.findByArchived(false);
+        List<Submission> submissions;
+        if (status == null) {
+            submissions = submissionRepository.findByArchived(false);
+        } else {
+            if (status.equalsIgnoreCase("OTHER")) {
+                submissions = SubmissionsUtil.filterForOther(submissionRepository.findByArchived(false));
+            } else {
+                if (status.equalsIgnoreCase("READY_TO_IMPORT")) {
+                    submissions = SubmissionsUtil.filterForReadyToImport(submissionRepository.findByOverallStatusAndArchived(Status.SUBMITTED.name(), false));
+                } else {
+                    submissions = submissionRepository.findByOverallStatusAndArchived(status, false);
+                }
+            }
+        }
+
         log.info("Found {} submissions.", submissions.size());
         return submissions;
     }

src/main/java/uk/ac/ebi/spot/gwas/deposition/ingest/util/SubmissionsUtil.java

@@ -0,0 +1,38 @@
+package uk.ac.ebi.spot.gwas.deposition.ingest.util;
+
+import uk.ac.ebi.spot.gwas.deposition.constants.Status;
+import uk.ac.ebi.spot.gwas.deposition.domain.Submission;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class SubmissionsUtil {
+
+    public static List<Submission> filterForOther(List<Submission> submissions) {
+        List<Submission> result = new ArrayList<>();
+        for (Submission submission : submissions) {
+            if (submission.getOverallStatus().equalsIgnoreCase(Status.CURATION_COMPLETE.name())) {
+                continue;
+            }
+            if (submission.getOverallStatus().equalsIgnoreCase(Status.SUBMITTED.name()) &&
+                    submission.getPublicationId() != null) {
+                continue;
+            }
+
+            result.add(submission);
+        }
+        return result;
+    }
+
+    public static List<Submission> filterForReadyToImport(List<Submission> submissions) {
+        List<Submission> result = new ArrayList<>();
+        for (Submission submission : submissions) {
+            if (submission.getPublicationId() == null) {
+                continue;
+            }
+
+            result.add(submission);
+        }
+        return result;
+    }
+}

src/test/java/uk/ac/ebi/spot/gwas/deposition/ingest/rest/SubmissionsControllerTest.java

@@ -143,6 +143,55 @@ public void shouldGetSubmissions() throws Exception {
         assertEquals(1, actual.get(0).getNotes().size());
     }
 
+    /**
+     * GET /v1/submissions
+     */
+    @Test
+    public void shouldGetSubmissionsByStatus() throws Exception {
+        Publication publication = publicationRepository.insert(TestUtil.publication());
+        Submission submission = new Submission(publication.getId(), SubmissionProvenanceType.PUBLICATION.name(),
+                new Provenance(DateTime.now(), user.getId()));
+        submission.setStudies(Arrays.asList(new String[]{study.getId()}));
+        submission.setNotes(Arrays.asList(new String[]{note.getId()}));
+        submission.setAssociations(Arrays.asList(new String[]{association.getId()}));
+        submission.setSamples(Arrays.asList(new String[]{sample.getId()}));
+        submission.setCompleted(true);
+        submission.setOverallStatus(Status.CURATION_COMPLETE.name());
+        submissionRepository.insert(submission);
+
+        String endpoint = GeneralCommon.API_V1 + IngestServiceConstants.API_SUBMISSIONS + "?status=SUBMITTED";
+
+        String response = mockMvc.perform(get(endpoint)
+                .contentType(MediaType.APPLICATION_JSON))
+                .andExpect(status().isOk())
+                .andReturn()
+                .getResponse()
+                .getContentAsString();
+
+        List<SubmissionDto> actual = mapper.readValue(response, new TypeReference<List<SubmissionDto>>() {
+        });
+        assertTrue(actual.isEmpty());
+
+
+        endpoint = GeneralCommon.API_V1 + IngestServiceConstants.API_SUBMISSIONS + "?status=CURATION_COMPLETE";
+
+        response = mockMvc.perform(get(endpoint)
+                .contentType(MediaType.APPLICATION_JSON))
+                .andExpect(status().isOk())
+                .andReturn()
+                .getResponse()
+                .getContentAsString();
+
+        actual = mapper.readValue(response, new TypeReference<List<SubmissionDto>>() {
+        });
+        assertEquals(1, actual.size());
+        assertEquals(publication.getPmid(), actual.get(0).getPublication().getPmid());
+        assertEquals(1, actual.get(0).getStudies().size());
+        assertEquals(1, actual.get(0).getAssociations().size());
+        assertEquals(1, actual.get(0).getSamples().size());
+        assertEquals(1, actual.get(0).getNotes().size());
+    }
+
     /**
      * GET /v1/submission-envelopes
      */