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

Example 6 with ValidationError

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

the class ErrorCreationServiceTest method testCheckRiskAllele.

@Test
public void testCheckRiskAllele() throws Exception {
    when(validationChecks.checkRiskAllele("CHR4456:89")).thenReturn("Value does not start with rs or contain -");
    ValidationError error1 = errorCreationService.checkRiskAllele("CHR4456:89");
    assertThat(error1).extracting("field", "error", "warning").contains("Risk Allele", "Value does not start with rs or contain -", true);
    when(validationChecks.checkRiskAllele("")).thenReturn("Value is empty");
    ValidationError error2 = errorCreationService.checkRiskAllele("");
    assertThat(error2).extracting("field", "error", "warning").contains("Risk Allele", "Value is empty", false);
    when(validationChecks.checkRiskAllele("rs1234-?")).thenReturn(null);
    ValidationError error3 = errorCreationService.checkRiskAllele("rs1234-?");
    assertThat(error3).extracting("field", "error", "warning").contains(null, null, false);
}

Example 7 with ValidationError

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

the class ValidationChecksBuilder method runAuthorLevelBetaChecks.

/**
     * Run author level beta checks on a row
     *
     * @param association row to be checked
     */
public Collection<ValidationError> runAuthorLevelBetaChecks(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 rangeNotFound = errorCreationService.checkRangeIsPresent(association.getRange());
    validationErrors.add(rangeNotFound);
    return ErrorProcessingService.checkForValidErrors(validationErrors);
}

Example 8 with ValidationError

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

the class ErrorCreationServiceTest method testCheckAssociationRiskFrequency.

@Test
public void testCheckAssociationRiskFrequency() throws Exception {
    when(validationChecks.checkRiskFrequency("10")).thenReturn("Value is invalid, value is not between 0 and 1");
    ValidationError error1 = errorCreationService.checkAssociationRiskFrequency("10");
    assertThat(error1).extracting("field", "error", "warning").contains("Risk element (allele, haplotype or SNPxSNP interaction) frequency in controls", "Value is invalid, value is not between 0 and 1", true);
    when(validationChecks.checkRiskFrequency("")).thenReturn("Value is empty");
    ValidationError error2 = errorCreationService.checkAssociationRiskFrequency("");
    assertThat(error2).extracting("field", "error", "warning").contains("Risk element (allele, haplotype or SNPxSNP interaction) frequency in controls", "Value is empty", true);
    when(validationChecks.checkRiskFrequency("0.78")).thenReturn(null);
    ValidationError error3 = errorCreationService.checkAssociationRiskFrequency("0.78");
    assertThat(error3).extracting("field", "error", "warning").contains(null, null, false);
}

Example 9 with ValidationError

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

the class ErrorCreationServiceTest method testCheckMantissaIsLessThan10.

@Test
public void testCheckMantissaIsLessThan10() throws Exception {
    when(validationChecks.checkMantissaIsLessThan10(25)).thenReturn("Value not valid i.e. greater than 9");
    ValidationError error1 = errorCreationService.checkMantissaIsLessThan10(25);
    assertThat(error1).extracting("field", "error", "warning").contains("P-value mantissa", "Value not valid i.e. greater than 9", false);
    when(validationChecks.checkMantissaIsLessThan10(6)).thenReturn(null);
    ValidationError error2 = errorCreationService.checkMantissaIsLessThan10(6);
    assertThat(error2).extracting("field", "error", "warning").contains(null, null, false);
}

Example 10 with ValidationError

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

the class ErrorCreationServiceTest method testCheckBetaValuesIsEmpty.

@Test
public void testCheckBetaValuesIsEmpty() throws Exception {
    when(validationChecks.checkValueIsEmpty(Matchers.anyFloat())).thenReturn("Value is not empty");
    ValidationError error1 = errorCreationService.checkBetaValuesIsEmpty(Matchers.anyFloat());
    assertThat(error1).extracting("field", "error", "warning").contains("Beta", "Value is not empty", false);
    Float nullValue = null;
    when(validationChecks.checkValueIsEmpty(nullValue)).thenReturn(null);
    ValidationError error2 = errorCreationService.checkBetaValuesIsEmpty(nullValue);
    assertThat(error2).extracting("field", "error", "warning").contains(null, null, false);
}