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

Example 11 with Gene

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

the class LociAttributesService method saveGene.

public Collection<Gene> saveGene(Collection<Gene> genes) {
    Collection<Gene> locusGenes = new ArrayList<Gene>();
    genes.forEach(gene -> {
        Gene geneInDatabase = geneRepository.findByGeneName(gene.getGeneName());
        if (geneInDatabase != null) {
            getLog().debug("Gene " + geneInDatabase.getGeneName() + " already exists in database");
            locusGenes.add(geneInDatabase);
        } else {
            getLog().debug("Gene " + gene.getGeneName() + " not found in database. Creating and saving new gene.");
            geneRepository.save(gene);
            locusGenes.add(gene);
        }
    });
    return locusGenes;
}

Example 12 with Gene

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

the class SingleSnpMultiSnpAssociationService method createForm.

// Creates form which we can then return to view for editing etc.
@Override
public SnpAssociationForm createForm(Association association) {
    SnpAssociationStandardMultiForm form = new SnpAssociationStandardMultiForm();
    // Set association ID
    form.setAssociationId(association.getId());
    // Set simple string and float association attributes
    form.setRiskFrequency(association.getRiskFrequency());
    form.setPvalueDescription(association.getPvalueDescription());
    form.setSnpType(association.getSnpType());
    form.setMultiSnpHaplotype(association.getMultiSnpHaplotype());
    form.setSnpApproved(association.getSnpApproved());
    form.setPvalueMantissa(association.getPvalueMantissa());
    form.setPvalueExponent(association.getPvalueExponent());
    form.setStandardError(association.getStandardError());
    form.setRange(association.getRange());
    form.setDescription(association.getDescription());
    // Set OR/Beta values
    form.setOrPerCopyNum(association.getOrPerCopyNum());
    form.setOrPerCopyRecip(association.getOrPerCopyRecip());
    form.setOrPerCopyRecipRange(association.getOrPerCopyRecipRange());
    form.setBetaNum(association.getBetaNum());
    form.setBetaUnit(association.getBetaUnit());
    form.setBetaDirection(association.getBetaDirection());
    // Add collection of Efo traits
    form.setEfoTraits(association.getEfoTraits());
    // For each locus get genes and risk alleles
    Collection<Locus> loci = association.getLoci();
    Collection<Gene> locusGenes = new ArrayList<>();
    Collection<RiskAllele> locusRiskAlleles = new ArrayList<RiskAllele>();
    // For multi-snp and standard snps we assume their is only one locus
    for (Locus locus : loci) {
        locusGenes.addAll(locus.getAuthorReportedGenes());
        locusRiskAlleles.addAll(locus.getStrongestRiskAlleles().stream().sorted((v1, v2) -> Long.compare(v1.getId(), v2.getId())).collect(Collectors.toList()));
        // There should only be one locus thus should be safe to set these here
        form.setMultiSnpHaplotypeNum(locus.getHaplotypeSnpCount());
        form.setMultiSnpHaplotypeDescr(locus.getDescription());
    }
    // Get name of gene and add to form
    Collection<String> authorReportedGenes = new ArrayList<>();
    for (Gene locusGene : locusGenes) {
        authorReportedGenes.add(locusGene.getGeneName());
    }
    form.setAuthorReportedGenes(authorReportedGenes);
    // Handle snp rows
    Collection<GenomicContext> snpGenomicContexts = new ArrayList<GenomicContext>();
    Collection<SingleNucleotidePolymorphism> snps = new ArrayList<>();
    List<SnpFormRow> snpFormRows = new ArrayList<SnpFormRow>();
    List<SnpMappingForm> snpMappingForms = new ArrayList<SnpMappingForm>();
    for (RiskAllele riskAllele : locusRiskAlleles) {
        SnpFormRow snpFormRow = new SnpFormRow();
        snpFormRow.setStrongestRiskAllele(riskAllele.getRiskAlleleName());
        SingleNucleotidePolymorphism snp = riskAllele.getSnp();
        snps.add(snp);
        String rsID = snp.getRsId();
        snpFormRow.setSnp(rsID);
        Collection<Location> locations = snp.getLocations();
        for (Location location : locations) {
            SnpMappingForm snpMappingForm = new SnpMappingForm(rsID, location);
            snpMappingForms.add(snpMappingForm);
        }
        // Set proxy if one is present
        Collection<String> proxySnps = new ArrayList<>();
        if (riskAllele.getProxySnps() != null) {
            for (SingleNucleotidePolymorphism riskAlleleProxySnp : riskAllele.getProxySnps()) {
                proxySnps.add(riskAlleleProxySnp.getRsId());
            }
        }
        snpFormRow.setProxySnps(proxySnps);
        snpGenomicContexts.addAll(genomicContextRepository.findBySnpId(snp.getId()));
        snpFormRows.add(snpFormRow);
    }
    form.setSnpMappingForms(snpMappingForms);
    form.setGenomicContexts(snpGenomicContexts);
    form.setSnps(snps);
    form.setSnpFormRows(snpFormRows);
    return form;
}

Example 13 with Gene

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

the class SnpAssociationTableViewService method createSnpAssociationTableView.

/**
     * Create object, from Association, that will be returned to view
     *
     * @param association Association object
     */
public SnpAssociationTableView createSnpAssociationTableView(Association association) {
    SnpAssociationTableView snpAssociationTableView = new SnpAssociationTableView();
    // For SNP interaction studies snp, proxy snps, risk alleles etc
    // should be separated by an 'x'
    String delimiter = "; ";
    if (association.getSnpInteraction()) {
        delimiter = " x ";
    }
    snpAssociationTableView.setAssociationId(association.getId());
    // For each locus relevant attributes
    Collection<Locus> loci = association.getLoci();
    Collection<String> allLociGenes = new ArrayList<>();
    Collection<String> allLociRiskAlleles = new ArrayList<String>();
    Collection<String> allLociSnps = new ArrayList<String>();
    Collection<String> allLociProxySnps = new ArrayList<String>();
    Collection<String> allLociRiskAlleleFrequencies = new ArrayList<String>();
    Collection<String> allLociSnpStatuses = new ArrayList<String>();
    // By looking at each locus in turn we can keep order in view
    for (Locus locus : loci) {
        // Store gene names, a locus can have a number of genes attached.
        // Per locus create a comma separated list and add to an array.
        // Further processing will then delimit this list
        // either by ; or 'x' depending on association type
        Collection<String> currentlocusGenes = new ArrayList<>();
        String commaSeparatedGenes = "";
        for (Gene gene : locus.getAuthorReportedGenes()) {
            currentlocusGenes.add(gene.getGeneName());
        }
        if (!currentlocusGenes.isEmpty()) {
            commaSeparatedGenes = String.join(", ", currentlocusGenes);
            allLociGenes.add(commaSeparatedGenes);
        } else {
            allLociGenes.add("NR");
        }
        //This sort ensures that haplotype SNPs are displayed in the correct order
        Collection<RiskAllele> ra = locus.getStrongestRiskAlleles().stream().sorted((v1, v2) -> Long.compare(v1.getId(), v2.getId())).collect(Collectors.toList());
        for (RiskAllele riskAllele : ra) {
            allLociRiskAlleles.add(riskAllele.getRiskAlleleName());
            // Based on assumption we only have one locus with a single risk allele attached
            if (!association.getMultiSnpHaplotype() && !association.getSnpInteraction()) {
                if (riskAllele.getRiskFrequency() != null && !riskAllele.getRiskFrequency().isEmpty()) {
                    allLociRiskAlleleFrequencies.add(riskAllele.getRiskFrequency());
                }
            }
            // SNPs attached to risk allele
            SingleNucleotidePolymorphism snp = riskAllele.getSnp();
            allLociSnps.add(snp.getRsId());
            // Set proxies if present
            Collection<String> currentLocusProxies = new ArrayList<>();
            String commaSeparatedProxies = "";
            if (riskAllele.getProxySnps() != null) {
                for (SingleNucleotidePolymorphism proxySnp : riskAllele.getProxySnps()) {
                    currentLocusProxies.add(proxySnp.getRsId());
                }
            }
            // Comma separate proxies in view
            if (!currentLocusProxies.isEmpty()) {
                commaSeparatedProxies = String.join(", ", currentLocusProxies);
                allLociProxySnps.add(commaSeparatedProxies);
            } else {
                allLociProxySnps.add("NR");
            }
            // Only required for SNP interaction studies
            if (association.getSnpInteraction() != null) {
                if (association.getSnpInteraction()) {
                    // Genome wide Vs Limited List
                    Collection<String> snpStatus = new ArrayList<>();
                    String commaSeparatedSnpStatus = "";
                    if (riskAllele.getLimitedList() != null) {
                        if (riskAllele.getLimitedList()) {
                            snpStatus.add("LL");
                        }
                    }
                    if (riskAllele.getGenomeWide() != null) {
                        if (riskAllele.getGenomeWide()) {
                            snpStatus.add("GW");
                        }
                    }
                    if (!snpStatus.isEmpty()) {
                        commaSeparatedSnpStatus = String.join(", ", snpStatus);
                        allLociSnpStatuses.add(commaSeparatedSnpStatus);
                    } else {
                        allLociSnpStatuses.add("NR");
                    }
                    // Allele risk frequency
                    if (riskAllele.getRiskFrequency() != null && !riskAllele.getRiskFrequency().isEmpty()) {
                        allLociRiskAlleleFrequencies.add(riskAllele.getRiskFrequency());
                    } else {
                        allLociRiskAlleleFrequencies.add("NR");
                    }
                }
            }
        }
    }
    // Create delimited strings for view
    String authorReportedGenes = null;
    if (allLociGenes.size() > 1) {
        authorReportedGenes = String.join(delimiter, allLociGenes);
    } else {
        authorReportedGenes = String.join("", allLociGenes);
    }
    snpAssociationTableView.setAuthorReportedGenes(authorReportedGenes);
    String strongestRiskAlleles = null;
    if (allLociRiskAlleles.size() > 1) {
        strongestRiskAlleles = String.join(delimiter, allLociRiskAlleles);
    } else {
        strongestRiskAlleles = String.join("", allLociRiskAlleles);
    }
    snpAssociationTableView.setStrongestRiskAlleles(strongestRiskAlleles);
    String associationSnps = null;
    if (allLociSnps.size() > 1) {
        associationSnps = String.join(delimiter, allLociSnps);
    } else {
        associationSnps = String.join("", allLociSnps);
    }
    snpAssociationTableView.setSnps(associationSnps);
    String associationProxies = null;
    if (allLociProxySnps.size() > 1) {
        associationProxies = String.join(delimiter, allLociProxySnps);
    } else {
        associationProxies = String.join("", allLociProxySnps);
    }
    snpAssociationTableView.setProxySnps(associationProxies);
    // Set both risk frequencies
    String associationRiskAlleleFrequencies = null;
    if (allLociRiskAlleleFrequencies.size() > 1) {
        associationRiskAlleleFrequencies = String.join(delimiter, allLociRiskAlleleFrequencies);
    } else {
        associationRiskAlleleFrequencies = String.join("", allLociRiskAlleleFrequencies);
    }
    snpAssociationTableView.setRiskAlleleFrequencies(associationRiskAlleleFrequencies);
    snpAssociationTableView.setAssociationRiskFrequency(association.getRiskFrequency());
    String associationSnpStatuses = null;
    if (allLociSnpStatuses.size() > 1) {
        associationSnpStatuses = String.join(delimiter, allLociSnpStatuses);
    } else {
        associationSnpStatuses = String.join("", allLociSnpStatuses);
    }
    snpAssociationTableView.setSnpStatuses(associationSnpStatuses);
    snpAssociationTableView.setPvalueMantissa(association.getPvalueMantissa());
    snpAssociationTableView.setPvalueExponent(association.getPvalueExponent());
    snpAssociationTableView.setPvalueDescription(association.getPvalueDescription());
    Collection<String> efoTraits = new ArrayList<>();
    for (EfoTrait efoTrait : association.getEfoTraits()) {
        efoTraits.add(efoTrait.getTrait());
    }
    String associationEfoTraits = null;
    associationEfoTraits = String.join(", ", efoTraits);
    snpAssociationTableView.setEfoTraits(associationEfoTraits);
    // Set OR values
    snpAssociationTableView.setOrPerCopyNum(association.getOrPerCopyNum());
    snpAssociationTableView.setOrPerCopyRecip(association.getOrPerCopyRecip());
    snpAssociationTableView.setOrPerCopyRecipRange(association.getOrPerCopyRecipRange());
    // Set beta values
    snpAssociationTableView.setBetaNum(association.getBetaNum());
    snpAssociationTableView.setBetaDirection(association.getBetaDirection());
    snpAssociationTableView.setBetaUnit(association.getBetaUnit());
    snpAssociationTableView.setRange(association.getRange());
    snpAssociationTableView.setDescription(association.getDescription());
    snpAssociationTableView.setStandardError(association.getStandardError());
    snpAssociationTableView.setAssociationType(association.getSnpType());
    if (association.getMultiSnpHaplotype() != null) {
        if (association.getMultiSnpHaplotype()) {
            snpAssociationTableView.setMultiSnpHaplotype("Yes");
        }
        if (!association.getMultiSnpHaplotype()) {
            snpAssociationTableView.setMultiSnpHaplotype("No");
        }
    }
    if (association.getSnpInteraction() != null) {
        if (association.getSnpInteraction()) {
            snpAssociationTableView.setSnpInteraction("Yes");
        }
        if (!association.getSnpInteraction()) {
            snpAssociationTableView.setSnpInteraction("No");
        }
    }
    if (association.getSnpApproved() != null) {
        if (association.getSnpApproved()) {
            snpAssociationTableView.setSnpApproved("Yes");
        }
        if (!association.getSnpApproved()) {
            snpAssociationTableView.setSnpApproved("No");
        }
    }
    // Get validation warnings
    snpAssociationTableView.setValidationWarnings(associationValidationReportService.getWarningSet(association.getId()));
    // Get mapping details
    if (association.getLastMappingPerformedBy() != null) {
        snpAssociationTableView.setLastMappingPerformedBy(association.getLastMappingPerformedBy());
    }
    snpAssociationTableView.setMappingStatus("false");
    if (association.getLastMappingDate() != null) {
        snpAssociationTableView.setMappingStatus("true");
    }
    if (association.getLastMappingDate() != null) {
        DateFormat df = new SimpleDateFormat("dd-MMM-yyyy HH:mm:ss");
        String dateOfLastMapping = df.format(association.getLastMappingDate());
        snpAssociationTableView.setLastMappingDate(dateOfLastMapping);
    }
    return snpAssociationTableView;
}

Example 14 with Gene

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

the class SnpInteractionAssociationService method createForm.

// Create a form to return to view from Association model object
@Override
public SnpAssociationForm createForm(Association association) {
    // Create form
    SnpAssociationInteractionForm form = new SnpAssociationInteractionForm();
    // Set simple string and boolean values
    form.setAssociationId(association.getId());
    form.setPvalueDescription(association.getPvalueDescription());
    form.setSnpType(association.getSnpType());
    form.setSnpApproved(association.getSnpApproved());
    form.setPvalueMantissa(association.getPvalueMantissa());
    form.setPvalueExponent(association.getPvalueExponent());
    form.setStandardError(association.getStandardError());
    form.setRange(association.getRange());
    form.setDescription(association.getDescription());
    form.setRiskFrequency(association.getRiskFrequency());
    // Set OR/Beta values
    form.setOrPerCopyNum(association.getOrPerCopyNum());
    form.setOrPerCopyRecip(association.getOrPerCopyRecip());
    form.setOrPerCopyRecipRange(association.getOrPerCopyRecipRange());
    form.setBetaNum(association.getBetaNum());
    form.setBetaUnit(association.getBetaUnit());
    form.setBetaDirection(association.getBetaDirection());
    // Add collection of Efo traits
    form.setEfoTraits(association.getEfoTraits());
    // Create form columns
    List<SnpFormColumn> snpFormColumns = new ArrayList<>();
    // For each locus get genes and risk alleles
    Collection<Locus> loci = association.getLoci();
    Collection<GenomicContext> snpGenomicContexts = new ArrayList<GenomicContext>();
    Collection<SingleNucleotidePolymorphism> snps = new ArrayList<SingleNucleotidePolymorphism>();
    List<SnpMappingForm> snpMappingForms = new ArrayList<SnpMappingForm>();
    // Create a column per locus
    if (loci != null && !loci.isEmpty()) {
        for (Locus locus : loci) {
            SnpFormColumn snpFormColumn = new SnpFormColumn();
            // Set genes
            Collection<String> authorReportedGenes = new ArrayList<>();
            for (Gene gene : locus.getAuthorReportedGenes()) {
                authorReportedGenes.add(gene.getGeneName());
            }
            snpFormColumn.setAuthorReportedGenes(authorReportedGenes);
            // Set risk allele
            Collection<RiskAllele> locusRiskAlleles = locus.getStrongestRiskAlleles();
            String strongestRiskAllele = null;
            String snp = null;
            Collection<String> proxySnps = new ArrayList<>();
            Boolean genomeWide = false;
            Boolean limitedList = false;
            String riskFrequency = null;
            // For snp x snp interaction studies should only have one risk allele per locus
            if (locusRiskAlleles != null && locusRiskAlleles.size() == 1) {
                for (RiskAllele riskAllele : locusRiskAlleles) {
                    strongestRiskAllele = riskAllele.getRiskAlleleName();
                    snp = riskAllele.getSnp().getRsId();
                    SingleNucleotidePolymorphism snp_obj = riskAllele.getSnp();
                    snps.add(snp_obj);
                    Collection<Location> locations = snp_obj.getLocations();
                    for (Location location : locations) {
                        SnpMappingForm snpMappingForm = new SnpMappingForm(snp, location);
                        snpMappingForms.add(snpMappingForm);
                    }
                    snpGenomicContexts.addAll(genomicContextRepository.findBySnpId(snp_obj.getId()));
                    // Set proxy
                    if (riskAllele.getProxySnps() != null) {
                        for (SingleNucleotidePolymorphism riskAlleleProxySnp : riskAllele.getProxySnps()) {
                            proxySnps.add(riskAlleleProxySnp.getRsId());
                        }
                    }
                    if (riskAllele.getGenomeWide() != null && riskAllele.getGenomeWide()) {
                        genomeWide = true;
                    }
                    if (riskAllele.getLimitedList() != null && riskAllele.getLimitedList()) {
                        limitedList = true;
                    }
                    riskFrequency = riskAllele.getRiskFrequency();
                }
            } else {
                throw new RuntimeException("More than one risk allele found for locus " + locus.getId() + ", this is not supported yet for SNP interaction associations");
            }
            // Set column attributes
            snpFormColumn.setStrongestRiskAllele(strongestRiskAllele);
            snpFormColumn.setSnp(snp);
            snpFormColumn.setProxySnps(proxySnps);
            snpFormColumn.setGenomeWide(genomeWide);
            snpFormColumn.setLimitedList(limitedList);
            snpFormColumn.setRiskFrequency(riskFrequency);
            snpFormColumns.add(snpFormColumn);
        }
    }
    form.setSnpMappingForms(snpMappingForms);
    form.setGenomicContexts(snpGenomicContexts);
    form.setSnps(snps);
    form.setSnpFormColumns(snpFormColumns);
    form.setNumOfInteractions(snpFormColumns.size());
    return form;
}

Example 15 with Gene

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

the class MappingService method doMapping.

private void doMapping(Association association, String eRelease) throws EnsemblMappingException {
    getLog().info("Mapping association: " + association.getId());
    // Map to store returned location data, this is used in
    // snpLocationMappingService to process all locations linked
    // to a single snp in one go
    Map<String, Set<Location>> snpToLocationsMap = new HashMap<>();
    // Collection to store all genomic contexts
    Collection<GenomicContext> allGenomicContexts = new ArrayList<>();
    // Collection to store all errors for one association
    Collection<String> associationPipelineErrors = new ArrayList<>();
    // For each loci get the SNP and author reported genes
    Collection<Locus> studyAssociationLoci = association.getLoci();
    for (Locus associationLocus : studyAssociationLoci) {
        Long locusId = associationLocus.getId();
        Collection<SingleNucleotidePolymorphism> snpsLinkedToLocus = singleNucleotidePolymorphismQueryService.findByRiskAllelesLociId(locusId);
        Collection<Gene> authorReportedGenesLinkedToSnp = associationLocus.getAuthorReportedGenes();
        // Get gene names
        Collection<String> authorReportedGeneNamesLinkedToSnp = new ArrayList<>();
        for (Gene authorReportedGeneLinkedToSnp : authorReportedGenesLinkedToSnp) {
            authorReportedGeneNamesLinkedToSnp.add(authorReportedGeneLinkedToSnp.getGeneName().trim());
        }
        // Pass rs_id and author reported genes to mapping component
        for (SingleNucleotidePolymorphism snpLinkedToLocus : snpsLinkedToLocus) {
            String snpRsId = snpLinkedToLocus.getRsId();
            EnsemblMappingResult ensemblMappingResult = new EnsemblMappingResult();
            // Try to map supplied data
            try {
                getLog().debug("Running mapping....");
                ensemblMappingResult = ensemblMappingPipeline.run_pipeline(snpRsId, authorReportedGeneNamesLinkedToSnp, eRelease);
            } catch (Exception e) {
                getLog().error("Encountered a " + e.getClass().getSimpleName() + " whilst trying to run mapping of SNP " + snpRsId + ", found in association: " + association.getId(), e);
                throw new EnsemblMappingException();
            }
            getLog().debug("Mapping complete");
            // First remove old locations and genomic contexts
            snpLocationMappingService.removeExistingSnpLocations(snpLinkedToLocus);
            snpGenomicContextMappingService.removeExistingGenomicContexts(snpLinkedToLocus);
            Collection<Location> locations = ensemblMappingResult.getLocations();
            Collection<GenomicContext> snpGenomicContexts = ensemblMappingResult.getGenomicContexts();
            ArrayList<String> pipelineErrors = ensemblMappingResult.getPipelineErrors();
            // Update functional class
            snpLinkedToLocus.setFunctionalClass(ensemblMappingResult.getFunctionalClass());
            snpLinkedToLocus.setLastUpdateDate(new Date());
            snpLinkedToLocus.setMerged(Long.valueOf(ensemblMappingResult.getMerged()));
            // Update the merge table
            if (ensemblMappingResult.getMerged() == 1) {
                String currentSnpId = ensemblMappingResult.getCurrentSnpId();
                SingleNucleotidePolymorphism currentSnp = singleNucleotidePolymorphismRepository.findByRsId(currentSnpId);
                // Add the current SingleNucleotidePolymorphism to the "merged" rsID
                if (currentSnp == null) {
                    currentSnp = new SingleNucleotidePolymorphism();
                    currentSnp.setRsId(currentSnpId);
                    currentSnp.setFunctionalClass(snpLinkedToLocus.getFunctionalClass());
                    singleNucleotidePolymorphismRepository.save(currentSnp);
                    currentSnp = singleNucleotidePolymorphismRepository.findByRsId(currentSnpId);
                }
                snpLinkedToLocus.setCurrentSnp(currentSnp);
            }
            singleNucleotidePolymorphismRepository.save(snpLinkedToLocus);
            // Store location information for SNP
            if (!locations.isEmpty()) {
                for (Location location : locations) {
                    // This would only occur is SNP has multiple locations
                    if (snpToLocationsMap.containsKey(snpRsId)) {
                        snpToLocationsMap.get(snpRsId).add(location);
                    } else // First time we see a SNP store the location
                    {
                        Set<Location> snpLocation = new HashSet<>();
                        snpLocation.add(location);
                        snpToLocationsMap.put(snpRsId, snpLocation);
                    }
                }
            } else {
                getLog().warn("Attempt to map SNP: " + snpRsId + " returned no location details");
                pipelineErrors.add("Attempt to map SNP: " + snpRsId + " returned no location details");
            }
            // Store genomic context data for snp
            if (!snpGenomicContexts.isEmpty()) {
                allGenomicContexts.addAll(snpGenomicContexts);
            } else {
                getLog().warn("Attempt to map SNP: " + snpRsId + " returned no mapped genes");
                pipelineErrors.add("Attempt to map SNP: " + snpRsId + " returned no mapped genes");
            }
            if (!pipelineErrors.isEmpty()) {
                associationPipelineErrors.addAll(pipelineErrors);
            }
        }
    }
    // Create association report based on whether there is errors or not
    if (!associationPipelineErrors.isEmpty()) {
        associationReportService.processAssociationErrors(association, associationPipelineErrors);
    } else {
        associationReportService.updateAssociationReportDetails(association);
    }
    // Save data
    if (!snpToLocationsMap.isEmpty()) {
        getLog().debug("Updating location details ...");
        snpLocationMappingService.storeSnpLocation(snpToLocationsMap);
        getLog().debug("Updating location details complete");
    }
    if (!allGenomicContexts.isEmpty()) {
        getLog().debug("Updating genomic context details ...");
        snpGenomicContextMappingService.processGenomicContext(allGenomicContexts);
        getLog().debug("Updating genomic context details complete");
    }
}