Examples with DepositionSubmission uk.ac.ebi.spot.goci.model.deposition.DepositionSubmission used on opensource projects

Example 1 with DepositionSubmission

use of uk.ac.ebi.spot.goci.model.deposition.DepositionSubmission in project goci by EBISPOT.

the class SubmissionController method importSubmission.

@CrossOrigin
@RequestMapping(value = "/{submissionID}", produces = MediaType.TEXT_HTML_VALUE, method = RequestMethod.POST)
public String importSubmission(@PathVariable String submissionID, Model model, HttpServletRequest request, RedirectAttributes redirectAttributes) {
    List<String> statusMessages = new ArrayList<>();
    List<String> errorMessages = new ArrayList<>();
    try {
        Map<String, Submission> submissionList = submissionService.getSubmissions();
        DepositionSubmission depositionSubmission = submissionService.getSubmission(submissionID);
        SecureUser currentUser = currentUserDetailsService.getUserFromRequest(request);
        boolean importInProgress = submissionImportProgressService.importInProgress(depositionSubmission.getSubmissionId());
        if (importInProgress) {
            statusMessages = Arrays.asList(new String[] { "Import is already in progress. Please wait." });
        } else {
            SubmissionImportProgress submissionImportProgress = submissionImportProgressService.createNewImport(currentUser.getEmail(), depositionSubmission.getSubmissionId());
            depositionSubmissionImportService.importSubmission(depositionSubmission, currentUser, submissionImportProgress.getId());
            statusMessages = Arrays.asList(new String[] { "Import task has been submitted. You will receive an email when it's done." });
        }
        model.addAttribute("submissions", submissionList.values());
    } catch (Exception e) {
        e.printStackTrace();
        StringWriter stringWriter = new StringWriter();
        e.printStackTrace(new PrintWriter(stringWriter));
        errorMessages.add(stringWriter.getBuffer().toString());
    }
    redirectAttributes.addFlashAttribute("errors", String.join("<br>", errorMessages));
    redirectAttributes.addFlashAttribute("changesSaved", String.join("<br>", statusMessages));
    return "redirect:/submissions/" + submissionID;
}

Example 2 with DepositionSubmission

use of uk.ac.ebi.spot.goci.model.deposition.DepositionSubmission in project goci by EBISPOT.

the class SubmissionController method buildSubmission.

private Submission buildSubmission(DepositionSubmission depositionSubmission) {
    Submission testSub = new Submission();
    testSub.setId(depositionSubmission.getSubmissionId());
    testSub.setImportStatus(Submission.ImportStatus.NOT_READY);
    if (depositionSubmission.getPublication() != null) {
        testSub.setPubMedID(depositionSubmission.getPublication().getPmid());
        testSub.setAuthor(depositionSubmission.getPublication().getFirstAuthor());
        testSub.setCurator(depositionSubmission.getCreated().getUser().getName());
        testSub.setStatus(depositionSubmission.getStatus());
        testSub.setTitle(depositionSubmission.getPublication().getTitle());
        testSub.setJournal(depositionSubmission.getPublication().getJournal());
        testSub.setCreated(depositionSubmission.getCreated().getTimestamp().toString(DateTimeFormat.forPattern("yyyy-MM-dd")));
        testSub.setPublicationStatus(depositionSubmission.getPublication().getStatus());
        testSub.setSubmissionType(DepositionUtil.getSubmissionType(depositionSubmission));
        testSub.setPublicationDate(depositionSubmission.getPublication().getPublicationDate());
        if (depositionSubmission.getPublication().getCorrespondingAuthor() != null) {
            DepositionAuthor author = depositionSubmission.getPublication().getCorrespondingAuthor();
            if (author.getGroup() != null) {
                testSub.setCorrespondingAuthor(author.getGroup());
            } else {
                testSub.setCorrespondingAuthor(author.getFirstName() + ' ' + author.getLastName());
            }
        }
        if (testSub.getSubmissionType().equals(Submission.SubmissionType.UNKNOWN)) {
            testSub.setStatus("REVIEW");
        }
    } else if (depositionSubmission.getBodyOfWork() != null) {
        if (depositionSubmission.getBodyOfWork().getFirstAuthor() != null) {
            if (depositionSubmission.getBodyOfWork().getFirstAuthor().getGroup() != null) {
                testSub.setAuthor(depositionSubmission.getBodyOfWork().getFirstAuthor().getGroup());
            } else {
                testSub.setAuthor(depositionSubmission.getBodyOfWork().getFirstAuthor().getFirstName() + ' ' + depositionSubmission.getBodyOfWork().getFirstAuthor().getLastName());
            }
        }
        if (depositionSubmission.getBodyOfWork().getCorrespondingAuthors() != null) {
            DepositionAuthor author = depositionSubmission.getBodyOfWork().getCorrespondingAuthors().get(0);
            if (author.getGroup() != null) {
                testSub.setCorrespondingAuthor(author.getGroup());
            } else {
                testSub.setCorrespondingAuthor(author.getFirstName() + ' ' + author.getLastName());
            }
        }
        testSub.setStatus(depositionSubmission.getStatus());
        testSub.setTitle(depositionSubmission.getBodyOfWork().getTitle());
        testSub.setJournal(depositionSubmission.getBodyOfWork().getJournal());
        testSub.setCreated(depositionSubmission.getCreated().getTimestamp().toString(DateTimeFormat.forPattern("yyyy-MM-dd")));
        testSub.setPublicationStatus(depositionSubmission.getBodyOfWork().getStatus());
        testSub.setSubmissionType(DepositionUtil.getSubmissionType(depositionSubmission));
        if (testSub.getSubmissionType().equals(Submission.SubmissionType.UNKNOWN)) {
            testSub.setStatus("REVIEW");
        }
    }
    boolean importInProgress = submissionImportProgressService.importInProgress(depositionSubmission.getSubmissionId());
    if (importInProgress) {
        testSub.setStatus("IMPORT_IN_PROGRESS");
    }
    if (testSub.getStatus().equalsIgnoreCase("SUBMITTED") && !testSub.getSubmissionType().equals(Submission.SubmissionType.PRE_PUBLISHED) && !testSub.getSubmissionType().equals(Submission.SubmissionType.UNKNOWN)) {
        testSub.setImportStatus(Submission.ImportStatus.READY);
    }
    return testSub;
}

Example 3 with DepositionSubmission

use of uk.ac.ebi.spot.goci.model.deposition.DepositionSubmission in project goci by EBISPOT.

the class SubmissionController method viewSubmission.

@RequestMapping(value = "/{submissionId}", produces = MediaType.TEXT_HTML_VALUE, method = RequestMethod.GET)
public String viewSubmission(Model model, @PathVariable String submissionId) {
    DepositionSubmission depositionSubmission = submissionService.getSubmission(submissionId);
    Submission submission = buildSubmission(depositionSubmission);
    model.addAttribute("submission", submission);
    model.addAttribute("submissionData", depositionSubmission);
    model.addAttribute("submissionError", submissionService.checkSubmissionErrors(depositionSubmission));
    try {
        model.addAttribute("submissionString", mapper.writeValueAsString(depositionSubmission));
    } catch (JsonProcessingException e) {
        e.printStackTrace();
    }
    return "single_submission";
}

Example 4 with DepositionSubmission

use of uk.ac.ebi.spot.goci.model.deposition.DepositionSubmission in project goci by EBISPOT.

the class DepositionSubmissionServiceImpl method getSubmissions.

@Override
public Map<String, DepositionSubmission> getSubmissions() {
    String url = "/submissions";
    Map<String, DepositionSubmission> submissionList = new TreeMap<>();
    Map<String, Integer> params = new HashMap<>();
    try {
        DepositionSubmission[] submissions = template.getForObject(depositionIngestUri + url, DepositionSubmission[].class, params);
        for (DepositionSubmission submission : submissions) {
            submissionList.put(submission.getSubmissionId(), submission);
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
    return submissionList;
}

Example 5 with DepositionSubmission

use of uk.ac.ebi.spot.goci.model.deposition.DepositionSubmission in project goci by EBISPOT.

the class DepositionSubmissionImportService method importSubmission.

@Async
@Transactional
public void importSubmission(DepositionSubmission depositionSubmission, SecureUser currentUser, Long submissionImportId) {
    ImportLog importLog = new ImportLog();
    getLog().info("Evaluating submission type for: {}", depositionSubmission.getSubmissionId());
    Submission.SubmissionType submissionType = DepositionUtil.getSubmissionType(depositionSubmission);
    getLog().info("Found submission type for: {}", submissionType.name());
    Curator curator = curatorRepository.findByEmail(currentUser.getEmail());
    String submissionID = depositionSubmission.getSubmissionId();
    getLog().info("[{}] Retrieving publication: {}", submissionID, depositionSubmission.getPublication().getPmid());
    Publication publication = publicationService.findByPumedId(depositionSubmission.getPublication().getPmid());
    getLog().info("[{}] Found publication: {}", submissionID, publication.getPubmedId());
    getLog().info("[{}] Looking for studies in the local DB ...", submissionID);
    Collection<Study> dbStudies = studyService.findByPublication(depositionSubmission.getPublication().getPmid());
    List<Long> dbStudyIds = dbStudies.stream().map(Study::getId).collect(Collectors.toList());
    getLog().info("[{}] Found {} studies: {}", submissionID, dbStudies.size(), dbStudyIds);
    List<DepositionStudyDto> studies = depositionSubmission.getStudies();
    List<String> gcsts = studies.stream().map(DepositionStudyDto::getAccession).collect(Collectors.toList());
    getLog().info("[{}] Found {} studies in the submission retrieved from the Deposition App: {}", submissionID, studies.size(), gcsts);
    boolean outcome = true;
    if (submissionType == Submission.SubmissionType.SUM_STATS) {
        // if submission type is SUM_STATS only
        getLog().info("[{}] Found SUM_STATS submission.", submissionID, studies.size());
        ImportLogStep importStep = importLog.addStep(new ImportLogStep("Publishing summary stats", submissionID));
        Pair<Boolean, List<String>> result = depositionStudyService.publishSummaryStats(studies, dbStudies);
        if (result.getLeft()) {
            importLog.updateStatus(importStep.getId(), ImportLog.SUCCESS);
            importLog.addErrors(result.getRight(), "Publishing summary stats");
            importStep = importLog.addStep(new ImportLogStep("Updating submission status: CURATION_COMPLETE", submissionID));
            String stepOutcome = ingestService.updateSubmissionStatus(depositionSubmission, "CURATION_COMPLETE", "PUBLISHED_WITH_SS");
            if (stepOutcome != null) {
                importLog.updateStatus(importStep.getId(), ImportLog.SUCCESS_WITH_WARNINGS);
                importLog.addWarning(stepOutcome, "Updating submission status: CURATION_COMPLETE");
            } else {
                importLog.updateStatus(importStep.getId(), ImportLog.SUCCESS);
            }
        } else {
            importLog.updateStatus(importStep.getId(), ImportLog.FAIL);
            importLog.addErrors(result.getRight(), "Publishing summary stats");
            outcome = false;
        }
    } else {
        ImportLogStep studiesStep = importLog.addStep(new ImportLogStep("Verifying studies", submissionID));
        if (studies != null) {
            // && dbStudies.size() == 1) { //only do this for un-curated publications
            importLog.updateStatus(studiesStep.getId(), ImportLog.SUCCESS);
            getLog().info("[{}] Validating associations ...", submissionID);
            ImportLogStep importStep = importLog.addStep(new ImportLogStep("Validating associations", submissionID));
            for (DepositionStudyDto studyDto : studies) {
                List<DepositionAssociationDto> associations = depositionSubmission.getAssociations();
                if (associations != null) {
                    List<String> errors = associationValidationService.validateAssociations(studyDto.getStudyTag(), studyDto.getAccession(), associations);
                    importLog.addWarnings(errors, "Validating associations");
                }
            }
            getLog().info("[{}] Associations validated. Found {} errors and {} warnings.", submissionID, importLog.getErrorList().size(), importLog.getWarnings().size());
            if (!importLog.getErrorList().isEmpty()) {
                importLog.updateStatus(importStep.getId(), ImportLog.FAIL);
                outcome = false;
            } else {
                importLog.updateStatus(importStep.getId(), ImportLog.SUCCESS);
                getLog().info("[{}] Deleting proxy studies created when the publication was initially imported.", submissionID);
                importStep = importLog.addStep(new ImportLogStep("Deleting proxy studies", submissionID));
                String result = depositionStudyService.deleteStudies(dbStudies, curator, currentUser);
                if (result != null) {
                    importLog.addError(result, "Deleting proxy studies");
                    importLog.updateStatus(importStep.getId(), ImportLog.FAIL);
                    outcome = false;
                } else {
                    importLog.updateStatus(importStep.getId(), ImportLog.SUCCESS);
                }
                if (outcome) {
                    outcome = studiesProcessingService.processStudies(depositionSubmission, currentUser, publication, curator, importLog);
                    if (outcome) {
                        getLog().info("[{}] Deleting unpublished studies and body of works.", submissionID);
                        importStep = importLog.addStep(new ImportLogStep("Deleting unpublished data", submissionID));
                        result = cleanupPrePublishedStudies(studies);
                        if (result != null) {
                            importLog.addWarning(result, "Deleting unpublished data");
                            importLog.updateStatus(importStep.getId(), ImportLog.SUCCESS_WITH_WARNINGS);
                        } else {
                            importLog.updateStatus(importStep.getId(), ImportLog.SUCCESS);
                        }
                        importStep = importLog.addStep(new ImportLogStep("Updating submission status: CURATION_COMPLETE", submissionID));
                        result = ingestService.updateSubmissionStatus(depositionSubmission, "CURATION_COMPLETE", "CURATION_STARTED");
                        if (result != null) {
                            importLog.addWarning(result, "Updating submission status: CURATION_COMPLETE");
                            importLog.updateStatus(importStep.getId(), ImportLog.SUCCESS_WITH_WARNINGS);
                        } else {
                            importLog.updateStatus(importStep.getId(), ImportLog.SUCCESS);
                        }
                    }
                }
            }
        } else {
            importLog.updateStatus(studiesStep.getId(), ImportLog.FAIL);
            importLog.addError("Submission [" + submissionID + "] has no studies", "Verifying studies");
            outcome = false;
        }
    }
    if (outcome) {
        if (depositionSubmission.getPublication().getCorrespondingAuthor() != null) {
            getLog().info("Creating Publication extensions for corresponding authors ...");
            PublicationExtension author = new PublicationExtension();
            author.setCorrespondingAuthorEmail(depositionSubmission.getPublication().getCorrespondingAuthor().getEmail());
            if (depositionSubmission.getPublication().getCorrespondingAuthor().getGroup() != null) {
                author.setCorrespondingAuthorName(depositionSubmission.getPublication().getCorrespondingAuthor().getGroup());
            } else {
                author.setCorrespondingAuthorName(depositionSubmission.getPublication().getCorrespondingAuthor().getFirstName() + ' ' + depositionSubmission.getPublication().getCorrespondingAuthor().getLastName());
            }
            publicationExtensionRepository.save(author);
            getLog().info("Publication extension created: {}", author.getId());
            List<PublicationExtension> authorList = new ArrayList<>();
            authorList.add(author);
            publication.setCorrespondingAuthors(authorList);
            publicationService.save(publication);
            getLog().info("Publication [{}] saved.", publication.getPubmedId());
        }
    } else {
        ImportLogStep importStep = importLog.addStep(new ImportLogStep("Updating submission status: IMPORT_FAILED", submissionID));
        String stepOutcome = ingestService.updateSubmissionStatus(depositionSubmission, "IMPORT_FAILED", "");
        if (stepOutcome != null) {
            importLog.updateStatus(importStep.getId(), ImportLog.FAIL);
            importLog.addError(stepOutcome, "Updating submission status: IMPORT_FAILED");
        } else {
            importLog.updateStatus(importStep.getId(), ImportLog.SUCCESS);
        }
    }
    mailService.sendSubmissionImportNotification(outcome, depositionSubmission.getPublication().getPmid(), submissionID, importLog, currentUser.getEmail());
    getLog().info("Import process finalized: {}", depositionSubmission.getSubmissionId());
    getLog().info(importLog.pretty(false));
    submissionImportProgressService.deleteImport(submissionImportId);
}