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

Example 11 with Association

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

the class PussycatGOCIController method setPvalueFilter.

private Filter setPvalueFilter(String pvalueMin, String pvalueMax) {
    double start_pvalue, end_pvalue;
    if (pvalueMin != null) {
        int startMantissaNum = Integer.parseInt(pvalueMin.split("e")[0]);
        int startExponentNum = Integer.parseInt(pvalueMin.split("e")[1]);
        start_pvalue = startMantissaNum * Math.pow(10, startExponentNum);
    } else {
        start_pvalue = 0.0;
    }
    if (pvalueMax != null) {
        int endMantissaNum = Integer.parseInt(pvalueMax.split("e")[0]);
        int endExponentNum = Integer.parseInt(pvalueMax.split("e")[1]);
        end_pvalue = endMantissaNum * Math.pow(10, endExponentNum);
    } else {
        end_pvalue = 1 * Math.pow(10, -5);
    }
    Association association = template(Association.class);
    Filter filter = refine(association).on(association.getPvalue()).hasValues(start_pvalue, end_pvalue);
    return filter;
}

Example 12 with Association

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

the class TestFilenameGenerator method testGenerator.

@Test
public void testGenerator() {
    int e1 = -8;
    int m1 = 5;
    double p1 = m1 * Math.pow(10, e1);
    Association association = template(Association.class);
    Filter f1 = refine(association).on(association.getPvalue()).hasValues(0.0, p1);
    Filter f2 = refine(association).on(association.getPvalue()).hasValues(0.0, p1);
    TestSession session = new TestSession();
    String n1 = session.generateFilename(f1);
    System.out.println(n1);
    String n2 = session.generateFilename(f2);
    System.out.println(n2);
    String n3 = session.generateFilename();
    System.out.println(n3);
    assertEquals(n1, n2);
    assertNotNull(n3);
}

Example 13 with Association

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

the class QueryManager method getAssociationForTraitAndBand.

public List<URI> getAssociationForTraitAndBand(SparqlTemplate sparqlTemplate, URI trait, URI bandIndividual, List<Filter> filters) {
    List<URI> results = new ArrayList<URI>();
    if (filters.size() == 0) {
        Object retrieved = checkCache("getAssociationsForTraitInBand", sparqlTemplate, trait, bandIndividual);
        if (retrieved != null) {
            return (List<URI>) retrieved;
        }
        List<URI> queryResults = sparqlTemplate.query(SparqlQueries.ASSOCIATIONS_FOR_TRAIT_AND_BAND, new URIMapper("association"), trait, bandIndividual);
        // de-duplicate results; should be handled by        List<URI> results = new ArrayList<URI>();
        for (URI queryResult : queryResults) {
            if (!results.contains(queryResult)) {
                results.add(queryResult);
            }
        }
        return cache(results, "getAssociationsForTraitInBand", sparqlTemplate, trait, bandIndividual);
    } else if (filters.size() == 1) {
        for (Filter filter : filters) {
            if (filter.getFilteredType().equals(Association.class)) {
                Object retrieved = checkCache("getAssociationsForTraitInBand", sparqlTemplate, trait, bandIndividual, filter.getFilteredValues().get(1), filter.getFilteredValues().get(0));
                if (retrieved != null) {
                    return (List<URI>) retrieved;
                }
                results.addAll(sparqlTemplate.query(SparqlQueries.ASSOCIATIONS_FOR_TRAIT_AND_BAND_PVALUE_FILTER, new URIMapper("association"), trait, bandIndividual, filter.getFilteredValues().get(1), filter.getFilteredValues().get(0)));
                return cache(results, "getAssociationsForTraitInBand", sparqlTemplate, trait, bandIndividual, filter.getFilteredValues().get(1), filter.getFilteredValues().get(0));
            } else if (filter.getFilteredType().equals(Study.class)) {
                Object retrieved = checkCache("getAssociationsForTraitInBand", sparqlTemplate, trait, bandIndividual, filter.getFilteredRange().to(), filter.getFilteredRange().from());
                if (retrieved != null) {
                    return (List<URI>) retrieved;
                }
                results.addAll(sparqlTemplate.query(SparqlQueries.ASSOCIATIONS_FOR_TRAIT_AND_BAND_DATE_FILTER, new URIMapper("association"), trait, bandIndividual, filter.getFilteredRange().to(), filter.getFilteredRange().from()));
                return cache(results, "getAssociationsForTraitInBand", sparqlTemplate, trait, bandIndividual, filter.getFilteredRange().to(), filter.getFilteredRange().from());
            }
        }
    } else {
        Object pval_min = null, pval_max = null, date_min = null, date_max = null;
        for (Filter filter : filters) {
            if (filter.getFilteredType().equals(Association.class)) {
                pval_min = filter.getFilteredValues().get(0);
                pval_max = filter.getFilteredValues().get(1);
            } else if (filter.getFilteredType().equals(Study.class)) {
                date_min = filter.getFilteredRange().from();
                date_max = filter.getFilteredRange().to();
            }
        }
        Object retrieved = checkCache("getAssociationsForTraitInBand", sparqlTemplate, trait, bandIndividual, pval_max, pval_min, date_max, date_min);
        if (retrieved != null) {
            return (List<URI>) retrieved;
        }
        results.addAll(sparqlTemplate.query(SparqlQueries.ASSOCIATIONS_FOR_TRAIT_AND_BAND_PVALUE_DATE_FILTER, new URIMapper("association"), trait, bandIndividual, pval_max, pval_min, date_max, date_min));
        return cache(results, "getAssociationsForTraitInBand", sparqlTemplate, trait, bandIndividual, pval_max, pval_min, date_max, date_min);
    }
    return cache(results, "getAssociationsForTraitInBand", sparqlTemplate, trait, bandIndividual);
}

Example 14 with Association

use of uk.ac.ebi.spot.goci.model.Association 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 15 with Association

use of uk.ac.ebi.spot.goci.model.Association 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);
    }
}