Examples with EnsemblMappingException uk.ac.ebi.spot.goci.exception.EnsemblMappingException used on opensource projects

Example 1 with EnsemblMappingException

use of uk.ac.ebi.spot.goci.exception.EnsemblMappingException 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 EnsemblMappingException

use of uk.ac.ebi.spot.goci.exception.EnsemblMappingException 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 EnsemblMappingException

use of uk.ac.ebi.spot.goci.exception.EnsemblMappingException 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 4 with EnsemblMappingException

use of uk.ac.ebi.spot.goci.exception.EnsemblMappingException in project goci by EBISPOT.

the class AssociationControllerTest method uploadStudySnpsFileWithMappingError.

@Test
public void uploadStudySnpsFileWithMappingError() throws Exception {
    // Create objects required for testing
    MockMultipartFile file = new MockMultipartFile("file", "filename.txt", "text/plain", "TEST".getBytes());
    // Stubbing
    when(studyRepository.findOne(Matchers.anyLong())).thenReturn(STUDY);
    when(currentUserDetailsService.getUserFromRequest(Matchers.any(HttpServletRequest.class))).thenReturn(SECURE_USER);
    when(associationUploadService.upload(file, STUDY, SECURE_USER)).thenThrow(EnsemblMappingException.class);
    Future<Boolean> f = mock(Future.class);
    HashMap<String, Object> sessionattr = new HashMap<String, Object>();
    sessionattr.put("fileName", file.getOriginalFilename());
    sessionattr.put("ensemblMappingFailure", true);
    sessionattr.put("exception", new EnsemblMappingException());
    sessionattr.put("future", f);
    mockMvc.perform(get("/studies/1234/associations/getUploadResults").sessionAttrs(sessionattr).param("studyId", "1234")).andDo(print()).andExpect(status().is2xxSuccessful()).andExpect(model().attributeExists("study")).andExpect(forwardedUrl("ensembl_mapping_failure"));
    verify(studyRepository, times(1)).findOne(Matchers.anyLong());
}

Example 5 with EnsemblMappingException

use of uk.ac.ebi.spot.goci.exception.EnsemblMappingException in project goci by EBISPOT.

the class AssociationUploadService method upload.

@Transactional(readOnly = false)
public List<AssociationUploadErrorView> upload(MultipartFile file, Study study, SecureUser user) throws IOException, EnsemblMappingException {
    int s = study.getEvents().size();
    if (s > 0) {
        getLog().trace("Study " + study.getId().toString() + " has " + s + " events");
    }
    // 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);
    }
}