Examples with CohortAnnotationDefinition org.pmiops.workbench.db.model.CohortAnnotationDefinition used on opensource projects

Example 1 with CohortAnnotationDefinition

use of org.pmiops.workbench.db.model.CohortAnnotationDefinition in project workbench by all-of-us.

the class CohortReviewServiceImpl method validateParticipantCohortAnnotation.

/**
 * Helper method to validate that requested annotations are proper.
 *
 * @param participantCohortAnnotation
 */
private void validateParticipantCohortAnnotation(ParticipantCohortAnnotation participantCohortAnnotation, CohortAnnotationDefinition cohortAnnotationDefinition) {
    if (cohortAnnotationDefinition.getAnnotationType().equals(AnnotationType.BOOLEAN)) {
        if (participantCohortAnnotation.getAnnotationValueBoolean() == null) {
            throw createBadRequestException(AnnotationType.BOOLEAN.name(), participantCohortAnnotation.getCohortAnnotationDefinitionId());
        }
    } else if (cohortAnnotationDefinition.getAnnotationType().equals(AnnotationType.STRING)) {
        if (StringUtils.isBlank(participantCohortAnnotation.getAnnotationValueString())) {
            throw createBadRequestException(AnnotationType.STRING.name(), participantCohortAnnotation.getCohortAnnotationDefinitionId());
        }
    } else if (cohortAnnotationDefinition.getAnnotationType().equals(AnnotationType.DATE)) {
        if (StringUtils.isBlank(participantCohortAnnotation.getAnnotationValueDateString())) {
            throw createBadRequestException(AnnotationType.DATE.name(), participantCohortAnnotation.getCohortAnnotationDefinitionId());
        }
        SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd");
        try {
            Date date = new Date(sdf.parse(participantCohortAnnotation.getAnnotationValueDateString()).getTime());
            participantCohortAnnotation.setAnnotationValueDate(date);
        } catch (ParseException e) {
            throw new BadRequestException(String.format("Invalid Request: Please provide a valid %s value (%s) for annotation defintion id: %s", AnnotationType.DATE.name(), sdf.toPattern(), participantCohortAnnotation.getCohortAnnotationDefinitionId()));
        }
    } else if (cohortAnnotationDefinition.getAnnotationType().equals(AnnotationType.INTEGER)) {
        if (participantCohortAnnotation.getAnnotationValueInteger() == null) {
            throw createBadRequestException(AnnotationType.INTEGER.name(), participantCohortAnnotation.getCohortAnnotationDefinitionId());
        }
    } else if (cohortAnnotationDefinition.getAnnotationType().equals(AnnotationType.ENUM)) {
        if (StringUtils.isBlank(participantCohortAnnotation.getAnnotationValueEnum())) {
            throw createBadRequestException(AnnotationType.ENUM.name(), participantCohortAnnotation.getCohortAnnotationDefinitionId());
        }
        List<CohortAnnotationEnumValue> enumValues = cohortAnnotationDefinition.getEnumValues().stream().filter(enumValue -> participantCohortAnnotation.getAnnotationValueEnum().equals(enumValue.getName())).collect(Collectors.toList());
        if (enumValues.isEmpty()) {
            throw createBadRequestException(AnnotationType.ENUM.name(), participantCohortAnnotation.getCohortAnnotationDefinitionId());
        }
        participantCohortAnnotation.setCohortAnnotationEnumValue(enumValues.get(0));
    }
}

Example 2 with CohortAnnotationDefinition

use of org.pmiops.workbench.db.model.CohortAnnotationDefinition in project workbench by all-of-us.

the class CohortReviewServiceImpl method saveParticipantCohortAnnotation.

@Override
public ParticipantCohortAnnotation saveParticipantCohortAnnotation(Long cohortReviewId, ParticipantCohortAnnotation participantCohortAnnotation) {
    CohortAnnotationDefinition cohortAnnotationDefinition = findCohortAnnotationDefinition(participantCohortAnnotation.getCohortAnnotationDefinitionId());
    validateParticipantCohortAnnotation(participantCohortAnnotation, cohortAnnotationDefinition);
    if (findParticipantCohortAnnotation(cohortReviewId, participantCohortAnnotation.getCohortAnnotationDefinitionId(), participantCohortAnnotation.getParticipantId()) != null) {
        throw new BadRequestException(String.format("Invalid Request: Cohort annotation definition exists for id: %s", participantCohortAnnotation.getCohortAnnotationDefinitionId()));
    }
    return participantCohortAnnotationDao.save(participantCohortAnnotation);
}

Example 3 with CohortAnnotationDefinition

use of org.pmiops.workbench.db.model.CohortAnnotationDefinition in project workbench by all-of-us.

the class CohortReviewServiceImplTest method saveParticipantCohortAnnotationBadRequestCohortAnnotationDefinitionExists.

@Test
public void saveParticipantCohortAnnotationBadRequestCohortAnnotationDefinitionExists() throws Exception {
    long cohortAnnotationDefinitionId = 1;
    long cohortReviewId = 1;
    long participantId = 1;
    ParticipantCohortAnnotation participantCohortAnnotation = new ParticipantCohortAnnotation().annotationValueBoolean(Boolean.TRUE).cohortAnnotationDefinitionId(cohortAnnotationDefinitionId).cohortReviewId(cohortReviewId).participantId(participantId);
    CohortAnnotationDefinition cohortAnnotationDefinition = createCohortAnnotationDefinition(cohortAnnotationDefinitionId, AnnotationType.BOOLEAN);
    when(cohortAnnotationDefinitionDao.findOne(cohortAnnotationDefinitionId)).thenReturn(cohortAnnotationDefinition);
    when(participantCohortAnnotationDao.findByCohortReviewIdAndCohortAnnotationDefinitionIdAndParticipantId(cohortReviewId, cohortAnnotationDefinitionId, participantId)).thenReturn(participantCohortAnnotation);
    try {
        cohortReviewService.saveParticipantCohortAnnotation(cohortReviewId, participantCohortAnnotation);
        fail("Should have thrown BadRequestException!");
    } catch (BadRequestException e) {
        assertEquals("Invalid Request: Cohort annotation definition exists for id: " + cohortAnnotationDefinitionId, e.getMessage());
    }
    verify(cohortAnnotationDefinitionDao).findOne(cohortAnnotationDefinitionId);
    verifyNoMoreMockInteractions();
}

Example 4 with CohortAnnotationDefinition

use of org.pmiops.workbench.db.model.CohortAnnotationDefinition in project workbench by all-of-us.

the class CohortReviewServiceImplTest method assertParticipantCohortAnnotationModifyBadRequest.

private void assertParticipantCohortAnnotationModifyBadRequest(Long annotationId, ParticipantCohortAnnotation participantCohortAnnotation, AnnotationType annotationType) {
    Long cohortAnnotationDefinitionId = participantCohortAnnotation.getCohortAnnotationDefinitionId();
    Long cohortReviewId = participantCohortAnnotation.getCohortReviewId();
    Long participantId = participantCohortAnnotation.getParticipantId();
    CohortAnnotationDefinition cohortAnnotationDefinition = createCohortAnnotationDefinition(cohortAnnotationDefinitionId, annotationType);
    when(participantCohortAnnotationDao.findByAnnotationIdAndCohortReviewIdAndParticipantId(annotationId, cohortReviewId, participantId)).thenReturn(participantCohortAnnotation);
    when(cohortAnnotationDefinitionDao.findOne(cohortAnnotationDefinitionId)).thenReturn(cohortAnnotationDefinition);
    try {
        cohortReviewService.updateParticipantCohortAnnotation(annotationId, cohortReviewId, participantId, new ModifyParticipantCohortAnnotationRequest());
        fail("Should have thrown BadRequestExcpetion!");
    } catch (BadRequestException e) {
        assertEquals("Invalid Request: Please provide a valid " + cohortAnnotationDefinition.getAnnotationType().name() + " value for annotation defintion id: " + cohortAnnotationDefinition.getCohortAnnotationDefinitionId(), e.getMessage());
    }
    verify(participantCohortAnnotationDao, atLeastOnce()).findByAnnotationIdAndCohortReviewIdAndParticipantId(annotationId, cohortReviewId, participantId);
    verify(cohortAnnotationDefinitionDao, atLeastOnce()).findOne(cohortAnnotationDefinitionId);
    verifyNoMoreMockInteractions();
}

Example 5 with CohortAnnotationDefinition

use of org.pmiops.workbench.db.model.CohortAnnotationDefinition in project workbench by all-of-us.

the class CohortReviewServiceImplTest method findCohortAnnotationDefinition.

@Test
public void findCohortAnnotationDefinition() throws Exception {
    long cohortAnnotationDefinitionId = 1;
    when(cohortAnnotationDefinitionDao.findOne(cohortAnnotationDefinitionId)).thenReturn(new CohortAnnotationDefinition());
    cohortReviewService.findCohortAnnotationDefinition(cohortAnnotationDefinitionId);
    verify(cohortAnnotationDefinitionDao).findOne(cohortAnnotationDefinitionId);
    verifyNoMoreMockInteractions();
}