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

Example 1 with SnpAssociationTableView

use of uk.ac.ebi.spot.goci.curation.model.SnpAssociationTableView 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 2 with SnpAssociationTableView

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

the class PrintControllerTest method viewPrintableDetailsOfStudy.

@Test
public void viewPrintableDetailsOfStudy() throws Exception {
    // Set up some basic views
    SnpAssociationTableView snpAssociationTableView1 = new SnpAssociationTableView();
    snpAssociationTableView1.setBetaNum((float) 0.012);
    SnpAssociationTableView snpAssociationTableView2 = new SnpAssociationTableView();
    snpAssociationTableView1.setOrPerCopyNum((float) 5.97);
    // Stub
    when(studyRepository.findOne(STUDY.getId())).thenReturn(STUDY);
    Collection<Ancestry> initialStudyAncestryDescriptions = new ArrayList<>();
    Collection<Ancestry> replicationStudyAncestryDescriptions = new ArrayList<>();
    initialStudyAncestryDescriptions.add(ETH1);
    replicationStudyAncestryDescriptions.add(ETH2);
    replicationStudyAncestryDescriptions.add(ETH3);
    when(ancestryRepository.findByStudyIdAndType(STUDY.getId(), "initial")).thenReturn(initialStudyAncestryDescriptions);
    when(ancestryRepository.findByStudyIdAndType(STUDY.getId(), "replication")).thenReturn(replicationStudyAncestryDescriptions);
    when(studyPrintService.generatePrintView(STUDY.getId())).thenReturn(Arrays.asList(snpAssociationTableView1, snpAssociationTableView2));
    MvcResult mvcResult = this.mockMvc.perform(get("/studies/101/printview").accept(MediaType.TEXT_HTML_VALUE)).andExpect(request().asyncStarted()).andExpect(request().asyncResult("study_printview")).andReturn();
    this.mockMvc.perform(asyncDispatch(mvcResult)).andExpect(status().isOk()).andExpect(forwardedUrl("study_printview")).andExpect(model().attributeExists("studiesToPrint")).andExpect(model().attribute("studiesToPrint", instanceOf(Hashtable.class)));
}

Example 3 with SnpAssociationTableView

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

the class StudyPrintService method generatePrintView.

public Collection<SnpAssociationTableView> generatePrintView(Long studyId) {
    // Get relevant study details
    Study studyToView = studyRepository.findOne(studyId);
    // Association information
    Collection<Association> associations = new ArrayList<>();
    associations.addAll(associationRepository.findByStudyId(studyId));
    // For our associations create a table view object and return
    Collection<SnpAssociationTableView> snpAssociationTableViews = new ArrayList<SnpAssociationTableView>();
    for (Association association : associations) {
        SnpAssociationTableView snpAssociationTableView = snpAssociationTableViewService.createSnpAssociationTableView(association);
        snpAssociationTableViews.add(snpAssociationTableView);
    }
    return snpAssociationTableViews;
}

Example 4 with SnpAssociationTableView

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

the class AssociationController method viewStudySnps.

/*  Study SNP/Associations */
// Generate list of SNP associations linked to a study
@RequestMapping(value = "/studies/{studyId}/associations", produces = MediaType.TEXT_HTML_VALUE, method = RequestMethod.GET)
public String viewStudySnps(Model model, @PathVariable Long studyId, @RequestParam(required = false) Long associationId) {
    // Get all associations for a study
    Collection<Association> associations = associationRepository.findByStudyId(studyId);
    // For our associations create a table view object and return
    Collection<SnpAssociationTableView> snpAssociationTableViews = new ArrayList<SnpAssociationTableView>();
    for (Association association : associations) {
        SnpAssociationTableView snpAssociationTableView = snpAssociationTableViewService.createSnpAssociationTableView(association);
        snpAssociationTableViews.add(snpAssociationTableView);
    }
    model.addAttribute("snpAssociationTableViews", snpAssociationTableViews);
    // Determine last viewed association
    LastViewedAssociation lastViewedAssociation = associationOperationsService.getLastViewedAssociation(associationId);
    model.addAttribute("lastViewedAssociation", lastViewedAssociation);
    // Pass back count of associations
    Integer totalAssociations = associations.size();
    model.addAttribute("totalAssociations", totalAssociations);
    // Also passes back study object to view so we can create links back to main study page
    model.addAttribute("study", studyRepository.findOne(studyId));
    return "study_association";
}

Example 5 with SnpAssociationTableView

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

the class PrintController method getStudyInfoToPrint.

protected ArrayList<Object> getStudyInfoToPrint(Study studyToPrint) {
    // Get relevant study details
    Long studyId = studyToPrint.getId();
    // Get association information
    Collection<SnpAssociationTableView> snpAssociationTableViews = studyPrintService.generatePrintView(studyId);
    // Get housekeeping and ancestry information
    Housekeeping housekeeping = studyToPrint.getHousekeeping();
    Collection<StudyNote> studyNotes = studyToPrint.getNotes();
    String initialSampleDescription = studyToPrint.getInitialSampleSize();
    String replicateSampleDescription = studyToPrint.getReplicateSampleSize();
    // Creating a Hashtable
    ArrayList<Object> infoToPrint = new ArrayList<Object>();
    infoToPrint.add(studyToPrint);
    infoToPrint.add(housekeeping);
    infoToPrint.add(initialSampleDescription);
    infoToPrint.add(replicateSampleDescription);
    infoToPrint.add(ancestryRepository.findByStudyIdAndType(studyId, "initial"));
    infoToPrint.add(ancestryRepository.findByStudyIdAndType(studyId, "replication"));
    infoToPrint.add(snpAssociationTableViews);
    infoToPrint.add(studyNotes);
    return infoToPrint;
}