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

Example 16 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 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 17 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 (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 {
                    ValidationError snpError = errorCreationService.checkSnp(riskAllele.getSnp().getRsId(), eRelease);
                    validationErrors.add(snpError);
                }
            });
        }
    }
    return ErrorProcessingService.checkForValidErrors(validationErrors);
}

Example 18 with ValidationError

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

the class AssociationFileUploadService method createAssociationSummary.

/**
     * Process uploaded file, create an association and return a list of its errors
     *
     * @param row             Row to validate and convert into an association
     * @param validationLevel level of validation to run
     */
private AssociationSummary createAssociationSummary(AssociationUploadRow row, String validationLevel, String eRelease) {
    getLog().info("Creating association summary for row " + row.getRowNumber());
    Association association = associationRowProcessor.createAssociationFromUploadRow(row);
    Collection<ValidationError> errors = validationService.runAssociationValidation(association, validationLevel, eRelease);
    AssociationSummary associationSummary = new AssociationSummary();
    associationSummary.setRowNumber(row.getRowNumber());
    associationSummary.setAssociation(association);
    associationSummary.setErrors(errors);
    return associationSummary;
}

Example 19 with ValidationError

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

the class AssociationUploadService method upload.

public List<AssociationUploadErrorView> upload(MultipartFile file, Study study, SecureUser user) throws IOException, EnsemblMappingException {
    // File errors will contain any validation errors and be returned to controller if any are found
    List<AssociationUploadErrorView> fileErrors = new ArrayList<>();
    String originalFilename = file.getOriginalFilename();
    getLog().info("Uploading file: ".concat(originalFilename));
    // Upload file
    try {
        uploadFile(file, study.getId());
        // Send file, including path, to SNP batch loader process
        File uploadedFile = studyFileService.getFileFromFileName(study.getId(), originalFilename);
        ValidationSummary validationSummary = associationFileUploadService.processAndValidateAssociationFile(uploadedFile, "full");
        if (validationSummary != null) {
            // Check if we have any row errors
            long rowErrorCount = validationSummary.getRowValidationSummaries().parallelStream().filter(rowValidationSummary -> !rowValidationSummary.getErrors().isEmpty()).count();
            // Errors found
            if (rowErrorCount > 0) {
                studyFileService.deleteFile(study.getId(), originalFilename);
                getLog().error("Row errors found in file: " + originalFilename);
                validationSummary.getRowValidationSummaries().forEach(rowValidationSummary -> fileErrors.addAll(processRowError(rowValidationSummary)));
            } else {
                // Determine if we have any errors rather than warnings
                // Errors prevent saving association
                List<ValidationError> allAssociationsErrors = new ArrayList<>();
                validationSummary.getAssociationSummaries().forEach(associationSummary -> allAssociationsErrors.addAll(associationSummary.getErrors()));
                long associationErrorCount = allAssociationsErrors.parallelStream().filter(validationError -> !validationError.getWarning()).count();
                if (associationErrorCount > 0) {
                    studyFileService.deleteFile(study.getId(), originalFilename);
                    getLog().error("Association errors found in file: " + originalFilename);
                    validationSummary.getAssociationSummaries().forEach(associationSummary -> fileErrors.addAll(processAssociationError(associationSummary)));
                } else {
                    Integer numberOfAssociations = validationSummary.getAssociationSummaries().size();
                    String description = numberOfAssociations.toString().concat(" associations created from upload of '").concat(originalFilename).concat("'");
                    createBatchUploadEvent(study, description, user);
                    saveAssociations(validationSummary.getAssociationSummaries(), study, user);
                }
            }
        }
        return fileErrors;
    } catch (IOException e) {
        throw new IOException(e);
    }
}

Example 20 with ValidationError

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

the class ValidationChecksBuilder method runNoEffectChecks.

/**
     * Run no effect checks on a row
     *
     * @param association row to be checked
     */
public Collection<ValidationError> runNoEffectChecks(Association association) {
    Collection<ValidationError> validationErrors = new ArrayList<>();
    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 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);
    ValidationError standardErrorFound = errorCreationService.checkStandardErrorIsEmpty(association.getStandardError());
    validationErrors.add(standardErrorFound);
    ValidationError descriptionFound = errorCreationService.checkDescriptionIsEmpty(association.getDescription());
    validationErrors.add(descriptionFound);
    return ErrorProcessingService.checkForValidErrors(validationErrors);
}