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

Example 21 with ValidationError

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

the class ValidationChecksBuilder method runAuthorLevelNoEffectChecks.

/**
     * Run no effect checks on a row
     *
     * @param association row to be checked
     */
public Collection<ValidationError> runAuthorLevelNoEffectChecks(Association association) {
    Collection<ValidationError> validationErrors = new ArrayList<>();
    ValidationError orFound = errorCreationService.checkOrEmpty(association.getOrPerCopyNum());
    validationErrors.add(orFound);
    ValidationError betaFound = errorCreationService.checkBetaValuesIsEmpty(association.getBetaNum());
    validationErrors.add(betaFound);
    ValidationError betaUnitFound = errorCreationService.checkBetaUnitIsEmpty(association.getBetaUnit());
    validationErrors.add(betaUnitFound);
    ValidationError betaDirectionFound = errorCreationService.checkBetaDirectionIsEmpty(association.getBetaDirection());
    validationErrors.add(betaDirectionFound);
    ValidationError rangeFound = errorCreationService.checkRangeIsEmpty(association.getRange());
    validationErrors.add(rangeFound);
    return ErrorProcessingService.checkForValidErrors(validationErrors);
}

Example 22 with ValidationError

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

the class ValidationChecksBuilder method runAuthorLevelOrChecks.

/**
     * Run OR checks on a row
     *
     * @param association association to be checked
     */
public Collection<ValidationError> runAuthorLevelOrChecks(Association association) {
    Collection<ValidationError> validationErrors = new ArrayList<>();
    ValidationError betaFoundForOr = errorCreationService.checkBetaValuesIsEmpty(association.getBetaNum());
    validationErrors.add(betaFoundForOr);
    ValidationError betaUnitFoundForOr = errorCreationService.checkBetaUnitIsEmpty(association.getBetaUnit());
    validationErrors.add(betaUnitFoundForOr);
    ValidationError betaDirectionFoundForOr = errorCreationService.checkBetaDirectionIsEmpty(association.getBetaDirection());
    validationErrors.add(betaDirectionFoundForOr);
    ValidationError rangeNotFound = errorCreationService.checkRangeIsPresent(association.getRange());
    validationErrors.add(rangeNotFound);
    return ErrorProcessingService.checkForValidErrors(validationErrors);
}

Example 23 with ValidationError

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

the class ValidationChecksBuilder method runRiskFrequencyChecks.

/**
     * Run risk frequency checks on association and the risk alleles linked to a locus
     *
     * @param association row to be checked
     */
public Collection<ValidationError> runRiskFrequencyChecks(Association association) {
    Collection<ValidationError> validationErrors = new ArrayList<>();
    // Check the association risk frequency
    validationErrors.add(errorCreationService.checkAssociationRiskFrequency(association.getRiskFrequency()));
    // Check risk frequency on alleles if its a SNP interaction association
    if (association.getSnpInteraction()) {
        for (Locus locus : association.getLoci()) {
            locus.getStrongestRiskAlleles().forEach(riskAllele -> {
                validationErrors.add(errorCreationService.checkAlleleRiskFrequency(riskAllele.getRiskFrequency()));
            });
        }
    }
    return ErrorProcessingService.checkForValidErrors(validationErrors);
}

Example 24 with ValidationError

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

the class ValidationChecksBuilder method runBetaChecks.

/**
     * Run Beta checks on a row
     *
     * @param association row to be checked
     */
public Collection<ValidationError> runBetaChecks(Association association) {
    Collection<ValidationError> validationErrors = new ArrayList<>();
    ValidationError betaIsPresent = errorCreationService.checkBetaIsPresentAndIsNotNegative(association.getBetaNum());
    validationErrors.add(betaIsPresent);
    ValidationError betaUnitNotFound = errorCreationService.checkBetaUnitIsPresent(association.getBetaUnit());
    validationErrors.add(betaUnitNotFound);
    ValidationError betaDirectionNotFound = errorCreationService.checkBetaDirectionIsPresent(association.getBetaDirection());
    validationErrors.add(betaDirectionNotFound);
    ValidationError orFound = errorCreationService.checkOrEmpty(association.getOrPerCopyNum());
    validationErrors.add(orFound);
    ValidationError orRecipFound = errorCreationService.checkOrRecipEmpty(association.getOrPerCopyRecip());
    validationErrors.add(orRecipFound);
    ValidationError orRecipRangeFound = errorCreationService.checkOrPerCopyRecipRangeIsEmpty(association.getOrPerCopyRecipRange());
    validationErrors.add(orRecipRangeFound);
    ValidationError rangeNotFound = errorCreationService.checkRangeIsPresent(association.getRange());
    validationErrors.add(rangeNotFound);
    return ErrorProcessingService.checkForValidErrors(validationErrors);
}

Example 25 with ValidationError

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

the class ValidationChecksBuilder method runAnnotationChecks.

/**
     * Run general checks on a row annotation
     *
     * @param association association to be checked
     */
public Collection<ValidationError> runAnnotationChecks(Association association) {
    Collection<ValidationError> validationErrors = new ArrayList<>();
    validationErrors.add(errorCreationService.checkSnpType(association.getSnpType()));
    if (association.getSnpInteraction()) {
        for (Locus locus : association.getLoci()) {
            locus.getStrongestRiskAlleles().forEach(riskAllele -> {
                Boolean genomeWide = riskAllele.getGenomeWide();
                Boolean limitedList = riskAllele.getLimitedList();
                validationErrors.add(errorCreationService.checkSnpStatusIsPresent(genomeWide, limitedList));
            });
        }
    }
    return ErrorProcessingService.checkForValidErrors(validationErrors);
}