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

Example 36 with Association

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

the class AssociationDownloadService method extractGeneticData.

private void extractGeneticData(Association association, StringBuilder line) {
    final StringBuilder strongestAllele = new StringBuilder();
    final StringBuilder reportedGenes = new StringBuilder();
    final StringBuilder rsId = new StringBuilder();
    final StringBuilder proxySnpsRsIds = new StringBuilder();
    final StringBuilder riskAlleleFrequency = new StringBuilder();
    // Set our delimiter for download spreadsheet
    final String delimiter;
    if (association.getSnpInteraction() != null && association.getSnpInteraction()) {
        delimiter = " x ";
    } else {
        delimiter = "; ";
    }
    // Interaction specific values
    if (association.getSnpInteraction() != null && association.getSnpInteraction()) {
        association.getLoci().forEach(locus -> {
            Collection<RiskAllele> ra = locus.getStrongestRiskAlleles().stream().sorted((v1, v2) -> Long.compare(v1.getId(), v2.getId())).collect(Collectors.toList());
            ra.forEach(riskAllele -> {
                if (riskAllele.getRiskFrequency() != null && !riskAllele.getRiskFrequency().isEmpty()) {
                    String frequency = riskAllele.getRiskFrequency();
                    setOrAppend(riskAlleleFrequency, frequency, delimiter);
                } else {
                    setOrAppend(riskAlleleFrequency, "NR", delimiter);
                }
            });
            Collection<String> currentLocusGenes = new ArrayList<>();
            String commaSeparatedGenes = "";
            locus.getAuthorReportedGenes().forEach(gene -> {
                currentLocusGenes.add(gene.getGeneName().trim());
            });
            if (!currentLocusGenes.isEmpty()) {
                commaSeparatedGenes = String.join(", ", currentLocusGenes);
                setOrAppend(reportedGenes, commaSeparatedGenes, delimiter);
            } else {
                setOrAppend(reportedGenes, "NR", delimiter);
            }
        });
    } else {
        // Single study or a haplotype
        association.getLoci().forEach(locus -> {
            Collection<RiskAllele> ra = locus.getStrongestRiskAlleles().stream().sorted((v1, v2) -> Long.compare(v1.getId(), v2.getId())).collect(Collectors.toList());
            ra.forEach(riskAllele -> {
                setOrAppend(riskAlleleFrequency, "", "");
            });
            locus.getAuthorReportedGenes().forEach(gene -> {
                setOrAppend(reportedGenes, gene.getGeneName().trim(), ", ");
            });
        });
    }
    // Set attributes common to all associations
    association.getLoci().forEach(locus -> {
        Collection<RiskAllele> ra = locus.getStrongestRiskAlleles().stream().sorted((v1, v2) -> Long.compare(v1.getId(), v2.getId())).collect(Collectors.toList());
        ra.forEach(riskAllele -> {
            setOrAppend(strongestAllele, riskAllele.getRiskAlleleName(), delimiter);
            SingleNucleotidePolymorphism snp = riskAllele.getSnp();
            setOrAppend(rsId, snp.getRsId(), delimiter);
            Collection<String> currentLocusProxies = new ArrayList<>();
            String colonSeparatedProxies = "";
            if (riskAllele.getProxySnps() != null) {
                for (SingleNucleotidePolymorphism proxySnp : riskAllele.getProxySnps()) {
                    currentLocusProxies.add(proxySnp.getRsId());
                }
            }
            if (!currentLocusProxies.isEmpty()) {
                colonSeparatedProxies = String.join(", ", currentLocusProxies);
                setOrAppend(proxySnpsRsIds, colonSeparatedProxies, delimiter);
            } else {
                setOrAppend(proxySnpsRsIds, "NR", delimiter);
            }
        });
    });
    line.append(reportedGenes.toString());
    line.append("\t");
    line.append(strongestAllele.toString());
    line.append("\t");
    line.append(rsId.toString());
    line.append("\t");
    line.append(proxySnpsRsIds.toString());
    line.append("\t");
    line.append(riskAlleleFrequency.toString());
    line.append("\t");
}

Example 37 with Association

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

the class AssociationEventsViewService method createViews.

@Override
public List<EventView> createViews(Long studyId) {
    List<EventView> views = new ArrayList<>();
    Collection<Association> associations = studyRepository.findOne(studyId).getAssociations();
    if (!associations.isEmpty()) {
        // For each association gather up the events into a collection of views
        associations.forEach(association -> {
            Collection<Event> events = association.getEvents();
            Long associationId = association.getId();
            Collection<SingleNucleotidePolymorphism> snps = singleNucleotidePolymorphismRepository.findByRiskAllelesLociAssociationId(associationId);
            String associationSummary;
            StringJoiner snpJoiner = new StringJoiner(", ");
            snps.forEach(singleNucleotidePolymorphism -> {
                snpJoiner.add(singleNucleotidePolymorphism.getRsId());
            });
            associationSummary = snpJoiner.toString();
            events.forEach(event -> {
                String eventName = eventTypeService.translateEventByEventType(event.getEventType());
                EventView eventView = new AssociationEventView(eventName, event.getEventDate(), associationId, event.getUser().getEmail(), associationSummary);
                views.add(eventView);
            });
        });
    }
    return views;
}

Example 38 with Association

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

the class StudyOperationsService method assignStudyStatus.

/**
     * Assign status to a study
     */
public String assignStudyStatus(Study study, StatusAssignment statusAssignment, SecureUser userFromRequest) {
    CurationStatus newStatus = curationStatusRepository.findOne(statusAssignment.getStatusId());
    CurationStatus currentStudyStatus = study.getHousekeeping().getCurationStatus();
    String message = null;
    // If the current and new status are different
    if (newStatus != null && newStatus != currentStudyStatus) {
        // Get housekeeping object and assign new status
        Housekeeping housekeeping = study.getHousekeeping();
        if (newStatus.getStatus().equals("Publish study")) {
            // Run pre-publish checks first
            Collection<Association> associations = associationRepository.findByStudyId(study.getId());
            message = publishStudyCheckService.runChecks(study, associations);
            // if checks pass then update the status and save objects
            if (message == null) {
                housekeeping.setCurationStatus(newStatus);
                updateStatus(study, housekeeping, userFromRequest);
            }
        } else {
            housekeeping.setCurationStatus(newStatus);
            updateStatus(study, housekeeping, userFromRequest);
        }
    } else {
        message = "Current status and new status are the same, no change required";
    }
    return message;
}