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

Example 1 with ValidationError

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

the class SheetProcessorImpl method readSheetRows.

// Read and parse uploaded spreadsheet
@Override
public Collection<AssociationUploadRow> readSheetRows(XSSFSheet sheet) {
    XSSFRow headerRow = sheet.getRow(0);
    Map<Integer, UploadFileHeader> headerRowMap = createHeaderMap(headerRow);
    // Create collection to store all newly created rows
    Collection<AssociationUploadRow> associationUploadRows = new ArrayList<>();
    Integer lastRow = sheet.getLastRowNum();
    Integer rowNum = 1;
    while (rowNum <= lastRow) {
        AssociationUploadRow associationUploadRow = new AssociationUploadRow();
        // Set row number so its consistent with numbering curator will see via Excel
        associationUploadRow.setRowNumber(rowNum + 1);
        XSSFRow row = sheet.getRow(rowNum);
        // If the row contains defined cell values
        if (row.getPhysicalNumberOfCells() > 0) {
            for (Map.Entry<Integer, UploadFileHeader> heading : headerRowMap.entrySet()) {
                Integer colNum = heading.getKey();
                UploadFileHeader headerName = heading.getValue();
                XSSFCell cell = row.getCell(colNum, Row.RETURN_BLANK_AS_NULL);
                if (cell != null) {
                    try {
                        switch(headerName) {
                            case GENES:
                                associationUploadRow.setAuthorReportedGene(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case SNP:
                                associationUploadRow.setSnp(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case EFFECT_ALLELE:
                                associationUploadRow.setStrongestAllele(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case SECONDARY_EFFECT_ALLELE:
                                associationUploadRow.setEffectAllele(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case OTHER_ALLELES:
                                associationUploadRow.setOtherAllele(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case PROXY_SNP:
                                associationUploadRow.setProxy(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case EFFECT_ELEMENT_FREQUENCY_IN_CONTROLS:
                                associationUploadRow.setAssociationRiskFrequency(SheetCellProcessingService.processStringValue(cell));
                                break;
                            case INDEPENDENT_SNP_EFFECT_ALLELE_FREQUENCY_IN_CONTROLS:
                                associationUploadRow.setRiskFrequency(SheetCellProcessingService.processStringValue(cell));
                                break;
                            case PVALUE_MANTISSA:
                                associationUploadRow.setPvalueMantissa(SheetCellProcessingService.processIntValues(cell));
                                break;
                            case PVALUE_EXPONENT:
                                associationUploadRow.setPvalueExponent(SheetCellProcessingService.processIntValues(cell));
                                break;
                            case PVALUE_DESCRIPTION:
                                associationUploadRow.setPvalueDescription(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case OR:
                                associationUploadRow.setOrPerCopyNum(SheetCellProcessingService.processFloatValues(cell));
                                break;
                            case OR_RECIPROCAL:
                                associationUploadRow.setOrPerCopyRecip(SheetCellProcessingService.processFloatValues(cell));
                                break;
                            case BETA:
                                associationUploadRow.setBetaNum(SheetCellProcessingService.processFloatValues(cell));
                                break;
                            case BETA_UNIT:
                                associationUploadRow.setBetaUnit(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case BETA_DIRECTION:
                                associationUploadRow.setBetaDirection(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case RANGE:
                                associationUploadRow.setRange(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case OR_RECIPROCAL_RANGE:
                                associationUploadRow.setOrPerCopyRecipRange(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case STANDARD_ERROR:
                                associationUploadRow.setStandardError(SheetCellProcessingService.processFloatValues(cell));
                                break;
                            case DESCRIPTION:
                                associationUploadRow.setDescription(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case MULTI_SNP_HAPLOTYPE:
                                associationUploadRow.setMultiSnpHaplotype(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case SNP_INTERACTION:
                                associationUploadRow.setSnpInteraction(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case SNP_STATUS:
                                associationUploadRow.setSnpStatus(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case SNP_TYPE:
                                associationUploadRow.setSnpType(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            case EFO_TRAITS:
                                associationUploadRow.setEfoTrait(SheetCellProcessingService.processMandatoryStringValue(cell));
                                break;
                            default:
                                getLog().warn("Column with unknown heading found in file.");
                                break;
                        }
                    } catch (CellProcessingException cpe) {
                        // Add an excel error to the list of the errors.
                        ValidationError cpeValidationError = new ValidationError(headerName.toString(), cpe.getMessage(), false, "excel");
                        associationUploadRow.addCellErrorType(cpeValidationError);
                    }
                }
            }
            associationUploadRows.add(associationUploadRow);
        }
        rowNum++;
    }
    return associationUploadRows;
}

Example 2 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 3 with ValidationError

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

the class ValidationChecksBuilder method runLociAttributeChecks.

/**
 * Run loci attributes checks on association
 *
 * @param association association to be checked
 */
public Collection<ValidationError> runLociAttributeChecks(Association association, String eRelease) {
    Collection<ValidationError> validationErrors = new ArrayList<>();
    if (association.getLoci() != null) {
        Set<String> associationGenes = new HashSet<>();
        Collection<ValidationError> geneErrors = new ArrayList<>();
        // Create a unique set of all locus genes
        for (Locus locus : association.getLoci()) {
            Set<String> locusGenes = new HashSet<>();
            if (!locus.getAuthorReportedGenes().isEmpty()) {
                locusGenes = locus.getAuthorReportedGenes().stream().map(Gene::getGeneName).collect(Collectors.toSet());
            }
            associationGenes.addAll(locusGenes);
        }
        // Check genes
        associationGenes.forEach(geneName -> {
            getLog().info("Checking gene: ".concat(geneName));
            ValidationError geneError = errorCreationService.checkGene(geneName, eRelease);
            if (geneError.getError() != null) {
                geneErrors.add(geneError);
            }
        });
        if (!geneErrors.isEmpty()) {
            validationErrors.addAll(geneErrors);
        }
        for (Locus locus : association.getLoci()) {
            Collection<RiskAllele> riskAlleles = locus.getStrongestRiskAlleles();
            // Check risk allele attributes
            riskAlleles.forEach(riskAllele -> {
                ValidationError riskAlleleError = errorCreationService.checkRiskAllele(riskAllele.getRiskAlleleName());
                validationErrors.add(riskAlleleError);
                // If gene is valid proceed to check gene and snp location
                if (geneErrors.isEmpty()) {
                    Set<String> locusGenes = locus.getAuthorReportedGenes().stream().map(Gene::getGeneName).collect(Collectors.toSet());
                    locusGenes.forEach(geneName -> {
                        getLog().info("Checking snp/gene location: ".concat(geneName).concat(" ").concat(riskAllele.getSnp().getRsId()));
                        ValidationError snpGeneLocationError = errorCreationService.checkSnpGeneLocation(riskAllele.getSnp().getRsId(), geneName, eRelease);
                        validationErrors.add(snpGeneLocationError);
                    });
                } else {
                    // Check snp is valid
                    ValidationError snpError = errorCreationService.checkSnp(riskAllele.getSnp().getRsId(), eRelease);
                    validationErrors.add(snpError);
                }
            });
        }
    }
    return ErrorProcessingService.checkForValidErrors(validationErrors);
}

Example 4 with ValidationError

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

the class ErrorCreationServiceTest method testCheckOrIsPresent.

@Test
public void testCheckOrIsPresent() throws Exception {
    when(validationChecks.checkOrIsPresent(null)).thenReturn("Value is empty");
    ValidationError error1 = errorCreationService.checkOrIsPresent((null));
    assertThat(error1).extracting("field", "error", "warning").contains("OR", "Value is empty", false);
    when(validationChecks.checkOrIsPresent((float) 1.23)).thenReturn(null);
    ValidationError error2 = errorCreationService.checkOrIsPresent((float) 1.23);
    assertThat(error2).extracting("field", "error", "warning").contains(null, null, false);
    Float f1 = (float) (0.0 / 0.0);
    when(validationChecks.checkOrIsPresent(f1)).thenReturn("Value is not number");
    ValidationError error3 = errorCreationService.checkOrIsPresent((f1));
    assertThat(error3).extracting("field", "error", "warning").contains("OR", "Value is not number", false);
}

Example 5 with ValidationError

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

the class ErrorCreationServiceTest method testCheckSnpType.

@Test
public void testCheckSnpType() throws Exception {
    when(validationChecks.checkSnpType("bigger")).thenReturn("Value does not contain novel or known");
    ValidationError error1 = errorCreationService.checkSnpType("bigger");
    assertThat(error1).extracting("field", "error", "warning").contains("SNP type", "Value does not contain novel or known", false);
    when(validationChecks.checkSnpType("novel")).thenReturn(null);
    ValidationError error2 = errorCreationService.checkSnpType("novel");
    assertThat(error2).extracting("field", "error", "warning").contains(null, null, false);
}