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

Example 1 with CurationStatus

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

the class StudyOperationsService method updateHousekeeping.

/**
     * Update housekeeping
     */
public String updateHousekeeping(Housekeeping housekeeping, Study study, SecureUser user) {
    CurationStatus newStatus = housekeeping.getCurationStatus();
    CurationStatus currentStudyStatus = study.getHousekeeping().getCurationStatus();
    Curator newCurator = housekeeping.getCurator();
    Curator currentCurator = study.getHousekeeping().getCurator();
    // If curator has changed, record the curator change event
    if (newCurator != null && newCurator != currentCurator) {
        recordStudyCuratorChange(study, user, newCurator);
    }
    // If the current and new status are different
    String message = null;
    if (newStatus != null && newStatus != currentStudyStatus) {
        if (newStatus.getStatus().equals("Publish study")) {
            // Run pre-publish checks first
            Collection<Association> associations = associationRepository.findByStudyId(study.getId());
            message = publishStudyCheckService.runChecks(study, associations);
            // if checks pass then update the status
            if (message == null) {
                updateStatus(study, housekeeping, user);
            } else // restore old status
            {
                housekeeping.setCurationStatus(currentStudyStatus);
                housekeepingOperationsService.saveHousekeeping(study, housekeeping);
            }
        } else {
            updateStatus(study, housekeeping, user);
        }
    } else {
        // Save housekeeping returned from form
        housekeepingOperationsService.saveHousekeeping(study, housekeeping);
    }
    return message;
}

Example 2 with CurationStatus

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

the class StudyOperationsService method unpublishStudy.

/**
     * Unpublish a study entry in the database
     *
     * @param studyId         ID of study to unpublish
     * @param unpublishReason Reason the study is being unpublished
     * @param user            User performing request
     */
public void unpublishStudy(Long studyId, UnpublishReason unpublishReason, SecureUser user) {
    Study study = studyRepository.findOne(studyId);
    // Before we unpublish the study get its associated housekeeping
    Long housekeepingId = study.getHousekeeping().getId();
    Housekeeping housekeepingAttachedToStudy = housekeepingRepository.findOne(housekeepingId);
    //Set the unpublishDate and a new lastUpdateDate in houskeeping
    java.util.Date unpublishDate = new java.util.Date();
    housekeepingAttachedToStudy.setCatalogUnpublishDate(unpublishDate);
    housekeepingAttachedToStudy.setLastUpdateDate(unpublishDate);
    //Set the reason for unpublishing
    housekeepingAttachedToStudy.setUnpublishReason(unpublishReason);
    housekeepingAttachedToStudy.setIsPublished(false);
    //Set the unpublised status in housekeeping
    CurationStatus status = curationStatusRepository.findByStatus("Unpublished from catalog");
    housekeepingAttachedToStudy.setCurationStatus(status);
    updateStatus(study, housekeepingAttachedToStudy, user);
}

Example 3 with CurationStatus

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

the class HousekeepingOperationsServiceTest method createHousekeeping.

@Test
public void createHousekeeping() throws Exception {
    // Stubbing
    when(curationStatusRepository.findByStatus("Awaiting Curation")).thenReturn(AWAITING_CURATION);
    when(curatorRepository.findByLastName("Level 1 Curator")).thenReturn(LEVEL_1_CURATOR);
    Housekeeping housekeeping = housekeepingOperationsService.createHousekeeping();
    verify(curationStatusRepository, times(1)).findByStatus("Awaiting Curation");
    verify(curatorRepository, times(1)).findByLastName("Level 1 Curator");
    verify(housekeepingRepository, times(1)).save(Matchers.any(Housekeeping.class));
    verifyZeroInteractions(studyRepository);
    // Assertions
    assertThat(housekeeping).extracting(curator -> curator.getCurator().getLastName()).contains("Level 1 Curator");
    assertThat(housekeeping).extracting(curationStatus -> curationStatus.getCurationStatus().getStatus()).contains("Awaiting Curation");
    assertThat(housekeeping.getStudyAddedDate()).isToday();
}

Example 4 with CurationStatus

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

the class HousekeepingOperationsService method createHousekeeping.

/**
 * Create study housekeeping
 */
public Housekeeping createHousekeeping() {
    // Create housekeeping object and create the study added date
    Housekeeping housekeeping = new Housekeeping();
    java.util.Date studyAddedDate = new java.util.Date();
    housekeeping.setStudyAddedDate(studyAddedDate);
    // Set status
    CurationStatus status = curationStatusRepository.findByStatus("Awaiting Curation");
    housekeeping.setCurationStatus(status);
    // Set curator
    Curator curator = curatorRepository.findByLastName("Level 1 Curator");
    housekeeping.setCurator(curator);
    // Save housekeeping
    housekeepingRepository.save(housekeeping);
    // Save housekeeping
    return housekeeping;
}

Example 5 with CurationStatus

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

the class StudyOperationsService method assignStudyStatus.

/**
     * Assign status to a study
     */
public String assignStudyStatus(Study study, StatusAssignment statusAssignment, SecureUser userFromRequest) {
    CurationStatus newStatus = curationStatusRepository.findOne(statusAssignment.getStatusId());
    CurationStatus currentStudyStatus = study.getHousekeeping().getCurationStatus();
    String message = null;
    // If the current and new status are different
    if (newStatus != null && newStatus != currentStudyStatus) {
        // Get housekeeping object and assign new status
        Housekeeping housekeeping = study.getHousekeeping();
        if (newStatus.getStatus().equals("Publish study")) {
            // Run pre-publish checks first
            Collection<Association> associations = associationRepository.findByStudyId(study.getId());
            message = publishStudyCheckService.runChecks(study, associations);
            // if checks pass then update the status and save objects
            if (message == null) {
                housekeeping.setCurationStatus(newStatus);
                updateStatus(study, housekeeping, userFromRequest);
            }
        } else {
            housekeeping.setCurationStatus(newStatus);
            updateStatus(study, housekeeping, userFromRequest);
        }
    } else {
        message = "Current status and new status are the same, no change required";
    }
    return message;
}