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

Example 1 with SnpAssociationStandardMultiForm

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

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

the class AssociationController method addMultiSnps.

@RequestMapping(value = "/studies/{studyId}/associations/add_multi", produces = MediaType.TEXT_HTML_VALUE, method = RequestMethod.POST)
public String addMultiSnps(@ModelAttribute("form") @Valid SnpAssociationStandardMultiForm snpAssociationStandardMultiForm, 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", snpAssociationStandardMultiForm);
        return "add_multi_snp_association";
    }
    // Check for errors in form that would prevent saving an association
    List<AssociationValidationView> rowErrors = associationOperationsService.checkSnpAssociationFormErrors(snpAssociationStandardMultiForm, measurementType);
    if (!rowErrors.isEmpty()) {
        model.addAttribute("errors", rowErrors);
        model.addAttribute("form", snpAssociationStandardMultiForm);
        model.addAttribute("criticalErrorsFound", true);
        return "add_multi_snp_association";
    } else {
        // Create an association object from details in returned form
        Association newAssociation = singleSnpMultiSnpAssociationService.createAssociation(snpAssociationStandardMultiForm);
        // Save and validate form
        String eRelease = ensemblRestTemplateService.getRelease();
        Collection<AssociationValidationView> errors = associationOperationsService.saveAssociationCreatedFromForm(study, newAssociation, 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) {
            model.addAttribute("errors", errors);
            model.addAttribute("form", snpAssociationStandardMultiForm);
            model.addAttribute("criticalErrorsFound", true);
            return "add_multi_snp_association";
        } else {
            return "redirect:/associations/" + newAssociation.getId();
        }
    }
}

Example 3 with SnpAssociationStandardMultiForm

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

the class AssociationController method performValidation.

@Async
private void performValidation(Model model, HttpSession session, Study study, SecureUser user) {
    Future<Boolean> future = executorService.submit(() -> {
        Collection<Association> studyAssociations = associationService.findAllByStudyId(study.getId());
        for (Association associationToValidate : studyAssociations) {
            if (!associationToValidate.getSnpApproved()) {
                String measurementType = associationOperationsService.determineIfAssociationIsOrType(associationToValidate);
                List<AssociationValidationView> criticalErrors = new ArrayList<>();
                if (associationToValidate.getSnpInteraction()) {
                    criticalErrors = associationOperationsService.checkSnpAssociationInteractionFormErrorsForView((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()) {
                    session.setAttribute("measurementType", measurementType);
                    // Get mapping details
                    session.setAttribute("mappingDetails", associationOperationsService.createMappingDetails(associationToValidate));
                    // Return any association errors
                    session.setAttribute("errors", criticalErrors);
                    session.setAttribute("criticalErrorsFound", true);
                    session.setAttribute("associationId", associationToValidate.getId());
                    break;
                } 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, user, 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) {
                        session.setAttribute("study", study);
                        session.setAttribute("measurementType", measurementType);
                        // Get mapping details for association we're editing
                        session.setAttribute("mappingDetails", associationOperationsService.createMappingDetails(associationToValidate));
                        session.setAttribute("errors", errors);
                        session.setAttribute("criticalErrorsFound", true);
                        session.setAttribute("associationId", associationToValidate.getId());
                        break;
                    }
                }
            }
        }
        session.setAttribute("done", true);
        return true;
    });
    session.setAttribute("future", future);
}

Example 4 with SnpAssociationStandardMultiForm

use of uk.ac.ebi.spot.goci.curation.model.SnpAssociationStandardMultiForm 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.checkSnpAssociationInteractionFormErrorsForView(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 5 with SnpAssociationStandardMultiForm

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

the class AssociationControllerTest method addStandardSnpsWithRowErrors.

@Test
public void addStandardSnpsWithRowErrors() throws Exception {
    // Row errors prevent saving
    AssociationValidationView associationValidationView = new AssociationValidationView("SNP", "Value is empty", false);
    List<AssociationValidationView> errors = Collections.singletonList(associationValidationView);
    // Stubbing
    when(studyRepository.findOne(Matchers.anyLong())).thenReturn(STUDY);
    when(associationOperationsService.checkSnpAssociationFormErrors(Matchers.any(SnpAssociationStandardMultiForm.class), Matchers.anyString())).thenReturn(errors);
    mockMvc.perform(post("/studies/1234/associations/add_standard").param("measurementType", "or")).andExpect(status().isOk()).andExpect(model().attribute("form", instanceOf(SnpAssociationStandardMultiForm.class))).andExpect(model().attribute("errors", instanceOf(List.class))).andExpect(model().attribute("errors", hasSize(1))).andExpect(model().attributeExists("study")).andExpect(model().attributeExists("measurementType")).andExpect(view().name("add_standard_snp_association"));
    // verify properties of bound object
    ArgumentCaptor<SnpAssociationStandardMultiForm> formArgumentCaptor = ArgumentCaptor.forClass(SnpAssociationStandardMultiForm.class);
    verify(associationOperationsService).checkSnpAssociationFormErrors(formArgumentCaptor.capture(), Matchers.anyString());
    verify(studyRepository, times(1)).findOne(Matchers.anyLong());
    verifyZeroInteractions(singleSnpMultiSnpAssociationService);
    verify(associationOperationsService, never()).saveAssociationCreatedFromForm(Matchers.any(Study.class), Matchers.any(Association.class), Matchers.any(SecureUser.class), Matchers.anyString());
    verifyZeroInteractions(currentUserDetailsService);
}