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

Example 1 with AssociationReport

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

the class AssociationReportService method updateAssociationReportDetails.

/**
     * This method is used when the mapping pipeline returns no errors. It removes any existing association reports and
     * replaces with a new one with no errors. This ensures errors from previous runs of the mapping pipeline do not
     * remain in database if they are no longer appearing as mapping pipeline errors.
     *
     * @param association association, used to create new association report
     */
public void updateAssociationReportDetails(Association association) {
    // Create association report object
    AssociationReport associationReport = new AssociationReport();
    associationReport.setLastUpdateDate(new Date());
    // Before setting link to association remove any existing reports linked to this association
    AssociationReport existingReport = associationReportRepository.findByAssociationId(association.getId());
    if (existingReport != null) {
        associationReportRepository.delete(existingReport);
    }
    associationReport.setAssociation(association);
    // Save association report
    associationReportRepository.save(associationReport);
}

Example 2 with AssociationReport

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

the class MapCatalogService method mapCatalogContents.

/**
     * Get all associations in database and map
     *
     * @param performer name of curator/job carrying out the mapping
     */
public void mapCatalogContents(String performer) throws EnsemblMappingException {
    // Get all old association reports so we can compare with new ones, do this before we remap
    Collection<AssociationReport> oldAssociationReports = associationReportRepository.findAll();
    // Get all associations via service
    Collection<Association> associations = associationService.findAllAssociations();
    getLog().info("Mapping all associations in database, total number: " + associations.size());
    try {
        mappingService.validateAndMapAllAssociations(associations, performer);
    } catch (EnsemblMappingException e) {
        throw new EnsemblMappingException("Attempt to map all associations failed", e);
    }
    mappingErrorComparisonService.compareOldVersusNewErrors(oldAssociationReports, false, 0, 0);
}

Example 3 with AssociationReport

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

the class MappingErrorComparisonService method compareOldVersusNewErrors.

/**
     * Method used to compare errors from a previous mapping run. Looking for SNPs with new errors, or SNPs with a
     * different type of error.
     *
     * @param oldErrors collection of all association reports in database before mapping to latest Ensembl release
     */
public void compareOldVersusNewErrors(Collection<AssociationReport> oldErrors, boolean isLSF, Integer min, Integer max) {
    // Find all the latest association reports containing mapping errors
    getLog().debug("Method used to compare errors from a previous mapping run");
    Collection<AssociationReport> newAssociationReports = getnewAssociationReports(isLSF, min, max);
    Map<Long, AssociationReport> associationIdToNewAssociationReportMap = createNewReportsMap(newAssociationReports);
    Collection<MappingErrorComparisonReport> comparisonReports = new ArrayList<>();
    // Create report
    for (AssociationReport oldErrorReport : oldErrors) {
        MappingErrorComparisonReport mappingErrorComparisonReport = new MappingErrorComparisonReport();
        // Establish association and study details
        Long associationId = oldErrorReport.getAssociation().getId();
        Study study = studyRepository.findByAssociationsId(associationId);
        String pubmedId = study.getPubmedId();
        Long studyId = study.getId();
        mappingErrorComparisonReport.setStudyId(studyId);
        mappingErrorComparisonReport.setAssociationId(associationId);
        mappingErrorComparisonReport.setPubmedId(pubmedId);
        // Compare errors
        AssociationReport newErrorReport = associationIdToNewAssociationReportMap.get(associationId);
        String oldSnpError = oldErrorReport.getSnpError();
        String newSnpError = newErrorReport.getSnpError();
        Boolean differenceInSnpErrors = compareDifferences(oldSnpError, newSnpError);
        if (differenceInSnpErrors) {
            mappingErrorComparisonReport.setOldSnpError(oldSnpError);
            mappingErrorComparisonReport.setNewSnpError(newSnpError);
        }
        String oldSnpGeneOnDiffChr = oldErrorReport.getSnpGeneOnDiffChr();
        String newSnpGeneOnDiffChr = newErrorReport.getSnpGeneOnDiffChr();
        Boolean differenceInSnpGeneOnDiffChr = compareDifferences(oldSnpGeneOnDiffChr, newSnpGeneOnDiffChr);
        if (differenceInSnpGeneOnDiffChr) {
            mappingErrorComparisonReport.setOldSnpGeneOnDiffChr(oldSnpGeneOnDiffChr);
            mappingErrorComparisonReport.setNewSnpGeneOnDiffChr(newSnpGeneOnDiffChr);
        }
        String oldNoGeneForSymbol = oldErrorReport.getNoGeneForSymbol();
        String newNoGeneForSymbol = newErrorReport.getNoGeneForSymbol();
        Boolean differenceNoGeneForSymbol = compareDifferences(oldNoGeneForSymbol, newNoGeneForSymbol);
        if (differenceNoGeneForSymbol) {
            mappingErrorComparisonReport.setOldNoGeneForSymbol(oldNoGeneForSymbol);
            mappingErrorComparisonReport.setNewNoGeneForSymbol(newNoGeneForSymbol);
        }
        String oldGeneError = oldErrorReport.getGeneError();
        String newGeneError = newErrorReport.getGeneError();
        Boolean differenceGeneError = compareDifferences(oldGeneError, newGeneError);
        if (differenceGeneError) {
            mappingErrorComparisonReport.setOldGeneError(oldGeneError);
            mappingErrorComparisonReport.setNewGeneError(newGeneError);
        }
        String oldRestServiceError = oldErrorReport.getRestServiceError();
        String newRestServiceError = newErrorReport.getRestServiceError();
        Boolean differenceRestServiceError = compareDifferences(oldRestServiceError, newRestServiceError);
        if (differenceRestServiceError) {
            mappingErrorComparisonReport.setOldRestServiceError(oldRestServiceError);
            mappingErrorComparisonReport.setNewRestServiceError(newRestServiceError);
        }
        String oldSuspectVariationError = oldErrorReport.getSuspectVariationError();
        String newSuspectVariationError = newErrorReport.getSuspectVariationError();
        Boolean differenceSuspectVariationError = compareDifferences(oldSuspectVariationError, newSuspectVariationError);
        if (differenceSuspectVariationError) {
            mappingErrorComparisonReport.setOldSuspectVariationError(oldSuspectVariationError);
            mappingErrorComparisonReport.setNewSuspectVariationError(newSuspectVariationError);
        }
        // Only add reports if a significant difference has been found
        if (differenceInSnpErrors || differenceInSnpGeneOnDiffChr || differenceNoGeneForSymbol || differenceGeneError || differenceRestServiceError || differenceSuspectVariationError) {
            comparisonReports.add(mappingErrorComparisonReport);
        }
    }
    getLog().debug("create file");
    createFile(comparisonReports);
}

Example 4 with AssociationReport

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

the class AssociationReportService method processAssociationErrors.

/**
     * Method used to format data returned from view via form so it can be stored in database
     *
     * @param association association, used to create new association report
     * @param errors      collection of errors returned from mapping pipeline
     */
public void processAssociationErrors(Association association, Collection<String> errors) {
    // Lists and maps use to translate errors
    List<String> listOfStandardEnsemblErrors = createStandardErrorList();
    Map<String, String> standardEnsemblErrorToErrorType = createErrorMap();
    Map<String, String> errorToErrorTypeMap = new HashMap<>();
    // Check list of standard errors to see if error returned from pipeline matches standard list
    for (String error : errors) {
        for (String standardEnsemblError : listOfStandardEnsemblErrors) {
            if (error.contains(standardEnsemblError)) {
                String errorType = standardEnsemblErrorToErrorType.get(standardEnsemblError);
                errorToErrorTypeMap.put(error, errorType);
            } else {
                // Check error message isn't already in list
                if (!errorToErrorTypeMap.containsKey(error)) {
                    errorToErrorTypeMap.put(error, "unknown type");
                }
            }
        }
    }
    // Populate arrays that will hold various errors
    Collection<String> snpErrors = new ArrayList<>();
    Collection<String> snpGeneOnDiffChrErrors = new ArrayList<>();
    Collection<String> noGeneForSymbolErrors = new ArrayList<>();
    Collection<String> restServiceErrors = new ArrayList<>();
    Collection<String> suspectVariationErrors = new ArrayList<>();
    Collection<String> geneErrors = new ArrayList<>();
    for (Map.Entry<String, String> entry : errorToErrorTypeMap.entrySet()) {
        String errorMessage = entry.getKey();
        String errorType = entry.getValue();
        switch(errorType) {
            case "restServiceError":
                restServiceErrors.add(errorMessage);
                break;
            case "suspectVariationError":
                suspectVariationErrors.add(errorMessage);
                break;
            case "snpError":
                snpErrors.add(errorMessage);
                break;
            case "snpGeneOnDiffChrError":
                snpGeneOnDiffChrErrors.add(errorMessage);
                break;
            case "noGeneForSymbolError":
                noGeneForSymbolErrors.add(errorMessage);
                break;
            case "geneError":
                geneErrors.add(errorMessage);
                break;
            default:
                getLog().warn("For association ID: " + association.getId() + ", cannot determine error type for error " + errorMessage);
                break;
        }
    }
    // Format errors into string so they can be stored in database
    String allSnpErrors = null;
    String allSnpGeneOnDiffChrErrors = null;
    String allNoGeneForSymbolErrors = null;
    String allRestServiceErrors = null;
    String allSuspectVariationErrors = null;
    String allGeneErrors = null;
    if (!snpErrors.isEmpty()) {
        allSnpErrors = String.join(", ", snpErrors);
    }
    if (!snpGeneOnDiffChrErrors.isEmpty()) {
        allSnpGeneOnDiffChrErrors = String.join(", ", snpGeneOnDiffChrErrors);
    }
    if (!noGeneForSymbolErrors.isEmpty()) {
        allNoGeneForSymbolErrors = String.join(", ", noGeneForSymbolErrors);
    }
    if (!restServiceErrors.isEmpty()) {
        allRestServiceErrors = String.join(", ", restServiceErrors);
    }
    if (!suspectVariationErrors.isEmpty()) {
        allSuspectVariationErrors = String.join(", ", suspectVariationErrors);
    }
    if (!geneErrors.isEmpty()) {
        allGeneErrors = String.join(", ", geneErrors);
    }
    // Create association report object
    AssociationReport associationReport = new AssociationReport();
    associationReport.setLastUpdateDate(new Date());
    associationReport.setSnpError(allSnpErrors);
    associationReport.setSnpGeneOnDiffChr(allSnpGeneOnDiffChrErrors);
    associationReport.setNoGeneForSymbol(allNoGeneForSymbolErrors);
    associationReport.setRestServiceError(allRestServiceErrors);
    associationReport.setSuspectVariationError(allSuspectVariationErrors);
    associationReport.setGeneError(allGeneErrors);
    // Before setting link to association check for any existing reports linked to this association
    AssociationReport existingReport = associationReportRepository.findByAssociationId(association.getId());
    if (existingReport != null) {
        associationReportRepository.delete(existingReport);
    }
    associationReport.setAssociation(association);
    // Save association report
    associationReportRepository.save(associationReport);
}

Example 5 with AssociationReport

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

the class CheckMappingService method checkAssociationMappingAssignment.

public Boolean checkAssociationMappingAssignment(Association association) {
    Boolean mappingAssigned = true;
    AssociationReport associationReport = association.getAssociationReport();
    if (associationReport == null) {
        mappingAssigned = false;
    }
    return mappingAssigned;
}