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

Example 1 with MappingErrorComparisonReport

use of uk.ac.ebi.spot.goci.model.MappingErrorComparisonReport 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 2 with MappingErrorComparisonReport

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

the class MappingErrorComparisonService method createFile.

/**
     * Create file from comparisons
     *
     * @param comparisonReports reports to output to file
     */
private void createFile(Collection<MappingErrorComparisonReport> comparisonReports) {
    StringBuilder output = new StringBuilder();
    if (comparisonReports.size() > 0) {
        String header = "Study ID\tAssociation ID\tPubmed ID\tOld SNP Error\tNew SNP Error\tOld Snp Gene On Diff Chr Error\tNew Snp Gene On Diff Chr Error\tOld No Gene For Symbol Error\tNew No Gene For Symbol\tOld Gene Error\tNew Gene Error\tOld Suspect Variation Error\tNew Suspect Variation Error\tOld Rest Service Error\tNew Rest Service Error\n";
        output.append(header);
        for (MappingErrorComparisonReport comparisonReport : comparisonReports) {
            StringBuilder line = new StringBuilder();
            // Study ID
            if (comparisonReport.getStudyId() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getStudyId());
            }
            line.append("\t");
            // Association ID
            if (comparisonReport.getAssociationId() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getAssociationId());
            }
            line.append("\t");
            // Pubmed ID
            if (comparisonReport.getPubmedId() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getPubmedId());
            }
            line.append("\t");
            // SNP_ERROR
            if (comparisonReport.getOldSnpError() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getOldSnpError());
            }
            line.append("\t");
            if (comparisonReport.getNewSnpError() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getNewSnpError());
            }
            line.append("\t");
            // SNP_GENE_ON_DIFF_CHR
            if (comparisonReport.getOldSnpGeneOnDiffChr() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getOldSnpGeneOnDiffChr());
            }
            line.append("\t");
            if (comparisonReport.getNewSnpGeneOnDiffChr() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getNewSnpGeneOnDiffChr());
            }
            line.append("\t");
            // NO_GENE_FOR_SYMBOL
            if (comparisonReport.getOldNoGeneForSymbol() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getOldNoGeneForSymbol());
            }
            line.append("\t");
            if (comparisonReport.getNewNoGeneForSymbol() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getNewNoGeneForSymbol());
            }
            line.append("\t");
            // GENE_ERROR
            if (comparisonReport.getOldGeneError() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getOldGeneError());
            }
            line.append("\t");
            if (comparisonReport.getNewGeneError() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getNewGeneError());
            }
            line.append("\t");
            // SUSPECT_VARIATION_ERROR
            if (comparisonReport.getOldSuspectVariationError() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getOldSuspectVariationError());
            }
            line.append("\t");
            if (comparisonReport.getNewSuspectVariationError() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getNewSuspectVariationError());
            }
            line.append("\t");
            // REST_SERVICE_ERROR
            if (comparisonReport.getOldRestServiceError() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getOldRestServiceError());
            }
            line.append("\t");
            if (comparisonReport.getNewRestServiceError() == null) {
                line.append("");
            } else {
                line.append(comparisonReport.getNewRestServiceError());
            }
            line.append("\t");
            // Add new line
            line.append("\n");
            output.append(line.toString());
        }
    } else {
        output.append("No changes in errors identified between current and previous Ensembl release.");
        getLog().info("No changes in errors identified between current and previous Ensembl release.");
    }
    // Create and write to file
    File outputFile = null;
    try {
        outputFile = report.getFile();
    } catch (IOException e) {
        getLog().info("Could not find file to write to errors to");
    }
    // If at this stage we haven't got a file create one and write to it
    if (!outputFile.exists()) {
        try {
            outputFile.createNewFile();
            getLog().info("Created file: " + outputFile);
        } catch (IOException e) {
            getLog().error("Could not create file");
        }
    }
    try (Writer writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(outputFile), "utf-8"))) {
        writer.write(String.valueOf(output));
    } catch (IOException e) {
        getLog().info("Could not write to " + outputFile);
    }
}