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

Example 1 with SnpAssociationInteractionForm

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

the class AssociationController method addSnpInteractionView.

// Generate a empty form page to add a interaction association
@RequestMapping(value = "/studies/{studyId}/associations/add_interaction", produces = MediaType.TEXT_HTML_VALUE, method = RequestMethod.GET)
public String addSnpInteractionView(Model model, @PathVariable Long studyId, @RequestParam(required = true) String measurementType) {
    // Return form object
    SnpAssociationInteractionForm emptyForm = new SnpAssociationInteractionForm();
    // Measurement type determines whether we render a OR/Beta form
    model.addAttribute("measurementType", measurementType);
    model.addAttribute("form", emptyForm);
    // Also passes back study object to view so we can create links back to main study page
    model.addAttribute("study", studyRepository.findOne(studyId));
    return "add_snp_interaction_association";
}

Example 2 with SnpAssociationInteractionForm

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

the class AssociationController method editAssociation.

//Edit existing association
// We tried to remap if the snp or genes changed.
// TODO : implement something for SNP:SNP iteration. Actually we remap.
@RequestMapping(value = "/associations/{associationId}", produces = MediaType.TEXT_HTML_VALUE, method = RequestMethod.POST)
public // TODO COULD REFACTOR TO JUST USE SUPERCLASS AS METHOD PARAMETER
String editAssociation(@ModelAttribute SnpAssociationStandardMultiForm snpAssociationStandardMultiForm, @ModelAttribute SnpAssociationInteractionForm snpAssociationInteractionForm, @PathVariable Long associationId, @RequestParam(value = "associationtype", required = true) String associationType, Model model, HttpServletRequest request, RedirectAttributes redirectAttributes) throws EnsemblMappingException {
    // Establish study and association we are editing
    Collection<String> previousAuthorReportedGenes = new HashSet<>();
    Collection<String> authorReportedGenes = new HashSet<>();
    Collection<String> previousSnps = new HashSet<>();
    Collection<String> snps = new HashSet<>();
    String isToRemapping = "yes";
    Association associationToEdit = associationRepository.findOne(associationId);
    Long studyId = associationToEdit.getStudy().getId();
    Study study = studyRepository.findOne(studyId);
    model.addAttribute("study", study);
    AssociationReport oldAssociationReport = associationToEdit.getAssociationReport();
    previousAuthorReportedGenes = associationOperationsService.getGenesIds(associationToEdit.getLoci());
    previousSnps = associationOperationsService.getSpnsName(associationToEdit.getSnps());
    // Determine if association is an OR or BETA type
    String measurementType = associationOperationsService.determineIfAssociationIsOrType(associationToEdit);
    model.addAttribute("measurementType", measurementType);
    // Validate returned form depending on association type
    List<AssociationValidationView> criticalErrors = new ArrayList<>();
    if (associationType.equalsIgnoreCase("interaction")) {
        criticalErrors = associationOperationsService.checkSnpAssociationInteractionFormErrors(snpAssociationInteractionForm, measurementType);
    } else {
        criticalErrors = associationOperationsService.checkSnpAssociationFormErrors(snpAssociationStandardMultiForm, measurementType);
    }
    // If errors found then return the edit form with all information entered by curator preserved
    if (!criticalErrors.isEmpty()) {
        // Get mapping details
        model.addAttribute("mappingDetails", associationOperationsService.createMappingDetails(associationToEdit));
        // Return any association errors
        model.addAttribute("errors", criticalErrors);
        model.addAttribute("criticalErrorsFound", true);
        if (associationType.equalsIgnoreCase("interaction")) {
            model.addAttribute("form", snpAssociationInteractionForm);
            return "edit_snp_interaction_association";
        } else {
            model.addAttribute("form", snpAssociationStandardMultiForm);
            // Determine view
            if (associationToEdit.getMultiSnpHaplotype()) {
                return "edit_multi_snp_association";
            } else {
                return "edit_standard_snp_association";
            }
        }
    } else {
        //Create association
        Association editedAssociation;
        // Request parameter determines how to process form and also which form to process
        if (associationType.equalsIgnoreCase("interaction")) {
            editedAssociation = snpInteractionAssociationService.createAssociation(snpAssociationInteractionForm);
        } else {
            editedAssociation = singleSnpMultiSnpAssociationService.createAssociation(snpAssociationStandardMultiForm);
            // New snps to compare with the previousSnps.
            Collection<SnpFormRow> newSnpsList = snpAssociationStandardMultiForm.getSnpFormRows();
            if (newSnpsList != null && !newSnpsList.isEmpty()) {
                for (SnpFormRow snp : newSnpsList) {
                    snps.add(snp.getSnp());
                }
            }
        }
        authorReportedGenes = associationOperationsService.getGenesIds(editedAssociation.getLoci());
        if (oldAssociationReport != null) {
            if ((previousAuthorReportedGenes.size() == authorReportedGenes.size()) && (snps.size() == snps.size())) {
                //check the values
                if ((authorReportedGenes.equals(previousAuthorReportedGenes)) && (snps.equals(previousSnps))) {
                    editedAssociation.setLastMappingDate(associationToEdit.getLastMappingDate());
                    editedAssociation.setLastMappingPerformedBy(associationToEdit.getLastMappingPerformedBy());
                    editedAssociation.setAssociationReport(oldAssociationReport);
                    isToRemapping = "no";
                }
            }
        }
        if ((oldAssociationReport != null) && (isToRemapping.compareTo("yes") == 0)) {
            associationOperationsService.deleteAssocationReport(associationToEdit.getAssociationReport().getId());
        }
        // Save and validate form
        String eRelease = ensemblRestTemplateService.getRelease();
        Collection<AssociationValidationView> errors = associationOperationsService.saveEditedAssociationFromForm(study, editedAssociation, associationId, currentUserDetailsService.getUserFromRequest(request), eRelease);
        // Determine if we have any errors rather than warnings
        long errorCount = errors.stream().filter(validationError -> !validationError.getWarning()).count();
        if (errorCount > 0) {
            // Get mapping details for association we're editing
            model.addAttribute("mappingDetails", associationOperationsService.createMappingDetails(associationToEdit));
            model.addAttribute("errors", errors);
            model.addAttribute("criticalErrorsFound", true);
            if (associationType.equalsIgnoreCase("interaction")) {
                model.addAttribute("form", snpAssociationInteractionForm);
                return "edit_snp_interaction_association";
            } else {
                model.addAttribute("form", snpAssociationStandardMultiForm);
                // Determine view
                if (associationToEdit.getMultiSnpHaplotype()) {
                    return "edit_multi_snp_association";
                } else {
                    return "edit_standard_snp_association";
                }
            }
        } else {
            redirectAttributes.addFlashAttribute("isToRemapping", isToRemapping);
            return "redirect:/associations/" + associationId;
        }
    }
}

Example 3 with SnpAssociationInteractionForm

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

the class AssociationController method validateUnapproved.

/**
     -     * Run mapping pipeline on all SNPs in a study
     -     *
     -     * @param studyId            Study ID in database
     -     * @param redirectAttributes attributes for a redirect scenario
     -     */
@RequestMapping(value = "/studies/{studyId}/associations/validate_unapproved", produces = MediaType.TEXT_HTML_VALUE, method = RequestMethod.GET)
public String validateUnapproved(@PathVariable Long studyId, RedirectAttributes redirectAttributes, Model model, HttpServletRequest request) throws //                                         @RequestParam(required = false) Long associationId)
EnsemblMappingException {
    Study study = studyRepository.findOne(studyId);
    // For the study get all associations
    Collection<Association> studyAssociations = associationRepository.findByStudyId(studyId);
    for (Association associationToValidate : studyAssociations) {
        if (!associationToValidate.getSnpApproved()) {
            String measurementType = associationOperationsService.determineIfAssociationIsOrType(associationToValidate);
            List<AssociationValidationView> criticalErrors = new ArrayList<>();
            if (associationToValidate.getSnpInteraction()) {
                criticalErrors = associationOperationsService.checkSnpAssociationInteractionFormErrors((SnpAssociationInteractionForm) associationOperationsService.generateForm(associationToValidate), measurementType);
            } else {
                criticalErrors = associationOperationsService.checkSnpAssociationFormErrors((SnpAssociationStandardMultiForm) associationOperationsService.generateForm(associationToValidate), measurementType);
            }
            //if an association has critical errors, go straight to that association
            if (!criticalErrors.isEmpty()) {
                model.addAttribute("study", study);
                model.addAttribute("measurementType", measurementType);
                // Get mapping details
                model.addAttribute("mappingDetails", associationOperationsService.createMappingDetails(associationToValidate));
                // Return any association errors
                model.addAttribute("errors", criticalErrors);
                model.addAttribute("criticalErrorsFound", true);
                if (associationToValidate.getSnpInteraction()) {
                    model.addAttribute("form", associationOperationsService.generateForm(associationToValidate));
                    return "redirect:/associations/" + associationToValidate.getId();
                // return "edit_snp_interaction_association";
                } else {
                    model.addAttribute("form", associationOperationsService.generateForm(associationToValidate));
                    // Determine view
                    if (associationToValidate.getMultiSnpHaplotype()) {
                        return "redirect:/associations/" + associationToValidate.getId();
                    // return "edit_multi_snp_association";
                    } else {
                        //                             return "edit_standard_snp_association";
                        return "redirect:/associations/" + associationToValidate.getId();
                    }
                }
            } else //     if there are no criticial errors, save the validation and go to the next association
            {
                // Save and validate form
                String eRelease = ensemblRestTemplateService.getRelease();
                Collection<AssociationValidationView> errors = associationOperationsService.validateAndSaveAssociation(study, associationToValidate, currentUserDetailsService.getUserFromRequest(request), eRelease);
                // Determine if we have any errors rather than warnings
                long errorCount = errors.stream().filter(validationError -> !validationError.getWarning()).count();
                //if there are errors rather than warnings, go straight to the page to edit
                if (errorCount > 0) {
                    model.addAttribute("study", study);
                    model.addAttribute("measurementType", measurementType);
                    // Get mapping details for association we're editing
                    model.addAttribute("mappingDetails", associationOperationsService.createMappingDetails(associationToValidate));
                    model.addAttribute("errors", errors);
                    model.addAttribute("criticalErrorsFound", true);
                    if (associationToValidate.getSnpInteraction()) {
                        model.addAttribute("form", associationOperationsService.generateForm(associationToValidate));
                        //                              return "edit_snp_interaction_association";
                        return "redirect:/associations/" + associationToValidate.getId();
                    } else {
                        model.addAttribute("form", associationOperationsService.generateForm(associationToValidate));
                        // Determine view
                        if (associationToValidate.getMultiSnpHaplotype()) {
                            //                                  return "edit_multi_snp_association";
                            return "redirect:/associations/" + associationToValidate.getId();
                        } else {
                            //                                  return "edit_standard_snp_association";
                            return "redirect:/associations/" + associationToValidate.getId();
                        }
                    }
                }
            }
        }
    }
    String message = "Mapping complete, please check for any errors displayed in the 'Errors' column";
    redirectAttributes.addFlashAttribute("mappingComplete", message);
    return "redirect:/studies/" + studyId + "/associations";
}

Example 4 with SnpAssociationInteractionForm

use of uk.ac.ebi.spot.goci.curation.model.SnpAssociationInteractionForm 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 5 with SnpAssociationInteractionForm

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

the class AssociationController method addSnpInteraction.

@RequestMapping(value = "/studies/{studyId}/associations/add_interaction", produces = MediaType.TEXT_HTML_VALUE, method = RequestMethod.POST)
public String addSnpInteraction(@ModelAttribute("form") @Valid SnpAssociationInteractionForm snpAssociationInteractionForm, BindingResult bindingResult, @PathVariable Long studyId, Model model, @RequestParam(required = true) String measurementType, HttpServletRequest request) throws EnsemblMappingException {
    Study study = studyRepository.findOne(studyId);
    model.addAttribute("study", study);
    model.addAttribute("measurementType", measurementType);
    // Binding vs Validator issue. File: messages.properties
    if (bindingResult.hasErrors()) {
        model.addAttribute("form", snpAssociationInteractionForm);
        return "add_snp_interaction_association";
    }
    // Check for errors in form that would prevent saving an association
    List<AssociationValidationView> colErrors = associationOperationsService.checkSnpAssociationInteractionFormErrors(snpAssociationInteractionForm, measurementType);
    if (!colErrors.isEmpty()) {
        model.addAttribute("errors", colErrors);
        model.addAttribute("form", snpAssociationInteractionForm);
        model.addAttribute("criticalErrorsFound", true);
        return "add_snp_interaction_association";
    } else {
        // Create an association object from details in returned form
        Association newAssociation = snpInteractionAssociationService.createAssociation(snpAssociationInteractionForm);
        // Save and validate form
        Collection<AssociationValidationView> errors = null;
        String eRelease = ensemblRestTemplateService.getRelease();
        try {
            errors = associationOperationsService.saveAssociationCreatedFromForm(study, newAssociation, currentUserDetailsService.getUserFromRequest(request), eRelease);
        } catch (EnsemblMappingException e) {
            return "ensembl_mapping_failure";
        }
        // Determine if we have any errors rather than warnings
        long errorCount = errors.stream().filter(validationError -> !validationError.getWarning()).count();
        if (errorCount > 0) {
            model.addAttribute("errors", errors);
            model.addAttribute("form", snpAssociationInteractionForm);
            model.addAttribute("criticalErrorsFound", true);
            return "add_snp_interaction_association";
        } else {
            return "redirect:/associations/" + newAssociation.getId();
        }
    }
}