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

Example 1 with ParticipantCohortAnnotation

use of org.pmiops.workbench.db.model.ParticipantCohortAnnotation 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 ParticipantCohortAnnotation

use of org.pmiops.workbench.db.model.ParticipantCohortAnnotation 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 3 with ParticipantCohortAnnotation

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

the class CohortReviewServiceImplTest method saveParticipantCohortAnnotationAllTypes.

@Test
public void saveParticipantCohortAnnotationAllTypes() throws Exception {
    long cohortAnnotationDefinitionId = 1;
    long cohortReviewId = 1;
    long participantId = 1;
    // Boolean Type
    ParticipantCohortAnnotation expectedAnnotation = new ParticipantCohortAnnotation().cohortAnnotationDefinitionId(cohortAnnotationDefinitionId).cohortReviewId(cohortReviewId).participantId(participantId).annotationValueBoolean(Boolean.TRUE);
    assertSaveParticipantCohortAnnotation(expectedAnnotation, AnnotationType.BOOLEAN);
    // Date Type
    SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd");
    expectedAnnotation = new ParticipantCohortAnnotation().cohortAnnotationDefinitionId(cohortAnnotationDefinitionId).cohortReviewId(cohortReviewId).participantId(participantId).annotationValueDateString("1999-02-01").annotationValueDate(new Date(sdf.parse("1999-02-01").getTime()));
    assertSaveParticipantCohortAnnotation(expectedAnnotation, AnnotationType.DATE);
    // Enum Type
    expectedAnnotation = new ParticipantCohortAnnotation().cohortAnnotationDefinitionId(cohortAnnotationDefinitionId).cohortReviewId(cohortReviewId).participantId(participantId).annotationValueEnum("enumValue");
    assertSaveParticipantCohortAnnotation(expectedAnnotation, AnnotationType.ENUM);
    // Integer Type
    expectedAnnotation = new ParticipantCohortAnnotation().cohortAnnotationDefinitionId(cohortAnnotationDefinitionId).cohortReviewId(cohortReviewId).participantId(participantId).annotationValueInteger(1);
    assertSaveParticipantCohortAnnotation(expectedAnnotation, AnnotationType.INTEGER);
    // String Type
    expectedAnnotation = new ParticipantCohortAnnotation().cohortAnnotationDefinitionId(cohortAnnotationDefinitionId).cohortReviewId(cohortReviewId).participantId(participantId).annotationValueString("String");
    assertSaveParticipantCohortAnnotation(expectedAnnotation, AnnotationType.STRING);
}

Example 4 with ParticipantCohortAnnotation

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

the class CohortReviewServiceImplTest method updateParticipantCohortAnnotationModifyNotFoundCohortAnnotationDefinition.

@Test
public void updateParticipantCohortAnnotationModifyNotFoundCohortAnnotationDefinition() throws Exception {
    long annotationId = 1;
    long cohortAnnotationDefinitionId = 1;
    long cohortReviewId = 1;
    long participantId = 1;
    ParticipantCohortAnnotation participantCohortAnnotation = new ParticipantCohortAnnotation().annotationValueBoolean(Boolean.TRUE).cohortAnnotationDefinitionId(cohortAnnotationDefinitionId).cohortReviewId(cohortReviewId).participantId(participantId);
    ModifyParticipantCohortAnnotationRequest modifyRequest = new ModifyParticipantCohortAnnotationRequest().annotationValueBoolean(Boolean.FALSE);
    when(participantCohortAnnotationDao.findByAnnotationIdAndCohortReviewIdAndParticipantId(annotationId, cohortReviewId, participantId)).thenReturn(participantCohortAnnotation);
    when(cohortAnnotationDefinitionDao.findOne(cohortAnnotationDefinitionId)).thenReturn(null);
    try {
        cohortReviewService.updateParticipantCohortAnnotation(annotationId, cohortReviewId, participantId, modifyRequest);
        fail("Should have thrown NotFoundException!");
    } catch (NotFoundException e) {
        assertEquals("Not Found: No cohort annotation definition found for id: " + cohortAnnotationDefinitionId, e.getMessage());
    }
    verify(participantCohortAnnotationDao).findByAnnotationIdAndCohortReviewIdAndParticipantId(annotationId, cohortReviewId, participantId);
    verify(cohortAnnotationDefinitionDao).findOne(cohortAnnotationDefinitionId);
    verifyNoMoreMockInteractions();
}

Example 5 with ParticipantCohortAnnotation

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

the class CohortReviewServiceImplTest method deleteParticipantCohortAnnotation.

@Test
public void deleteParticipantCohortAnnotation() throws Exception {
    long annotationId = 1;
    long cohortReviewId = 2;
    long participantId = 3;
    when(participantCohortAnnotationDao.findByAnnotationIdAndCohortReviewIdAndParticipantId(annotationId, cohortReviewId, participantId)).thenReturn(new ParticipantCohortAnnotation());
    cohortReviewService.deleteParticipantCohortAnnotation(annotationId, cohortReviewId, participantId);
    verify(participantCohortAnnotationDao).findByAnnotationIdAndCohortReviewIdAndParticipantId(annotationId, cohortReviewId, participantId);
    verifyNoMoreMockInteractions();
}