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

Example 1 with AssociationSummary

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

the class AssociationFileUploadService method createAssociationSummary.

/**
     * Process uploaded file, create an association and return a list of its errors
     *
     * @param row             Row to validate and convert into an association
     * @param validationLevel level of validation to run
     */
private AssociationSummary createAssociationSummary(AssociationUploadRow row, String validationLevel, String eRelease) {
    getLog().info("Creating association summary for row " + row.getRowNumber());
    Association association = associationRowProcessor.createAssociationFromUploadRow(row);
    Collection<ValidationError> errors = validationService.runAssociationValidation(association, validationLevel, eRelease);
    AssociationSummary associationSummary = new AssociationSummary();
    associationSummary.setRowNumber(row.getRowNumber());
    associationSummary.setAssociation(association);
    associationSummary.setErrors(errors);
    return associationSummary;
}

Example 2 with AssociationSummary

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

the class ValidationLogService method processErrors.

public void processErrors(File checkedFile, ValidationSummary validationSummary) {
    Collection<AssociationSummary> associationSummaries = validationSummary.getAssociationSummaries();
    Collection<RowValidationSummary> rowValidationSummaries = validationSummary.getRowValidationSummaries();
    /// Create the log file
    DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd'-T'HH-mm-ss");
    String now = dateFormat.format(new Date());
    String filePath = checkedFile.getParent();
    // If there is no file path just use current working dir
    if (filePath == null) {
        filePath = Paths.get(".").toAbsolutePath().normalize().toString();
    }
    String input_name = "";
    if (checkedFile.getName().contains(".xlsx")) {
        input_name = checkedFile.getName().replace(".xlsx", "");
    }
    String logName = filePath.concat(File.separator).concat(("Validation_results_").concat(input_name).concat("_").concat(now).concat(".txt"));
    System.out.println("Validation log written to " + logName);
    getLog().info("Validation log written to " + logName);
    // Write errors to file
    boolean fileCreationSuccess = false;
    File file = new File(logName);
    try {
        if (!file.exists()) {
            fileCreationSuccess = file.createNewFile();
        }
    } catch (IOException e) {
        getLog().error("Creating validation log failed");
        e.printStackTrace();
    }
    if (fileCreationSuccess) {
        FileWriter fw = null;
        try {
            fw = new FileWriter(file.getAbsoluteFile());
        } catch (IOException e) {
            getLog().error("Accessing validation log failed");
            e.printStackTrace();
        }
        BufferedWriter bw = new BufferedWriter(fw);
        try {
            writeErrorToFile(bw, associationSummaries, rowValidationSummaries);
        } catch (IOException e) {
            getLog().error("Writing to validation log failed");
            e.printStackTrace();
        }
    } else {
        getLog().error("Creating validation log failed");
    }
}

Example 3 with AssociationSummary

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

the class AssociationUploadService method upload.

public List<AssociationUploadErrorView> upload(MultipartFile file, Study study, SecureUser user) throws IOException, EnsemblMappingException {
    // 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);
    }
}

Example 4 with AssociationSummary

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

the class AssociationFileUploadService method processAndValidateAssociationFile.

/**
     * Process uploaded file and return a list of errors
     *
     * @param file XLSX file supplied by user
     */
public ValidationSummary processAndValidateAssociationFile(File file, String validationLevel) throws FileNotFoundException, SheetProcessingException {
    ValidationSummary validationSummary = new ValidationSummary();
    Collection<RowValidationSummary> rowValidationSummaries = new ArrayList<>();
    Collection<AssociationSummary> associationSummaries = new ArrayList<>();
    Collection<AssociationUploadRow> fileRows = new ArrayList<>();
    if (file.exists()) {
        // Create sheet
        XSSFSheet sheet = null;
        try {
            // Create a sheet for reading
            sheet = sheetCreationService.createSheet(file.getAbsolutePath());
            // Process file, depending on validation level, into a generic row object
            UploadSheetProcessor uploadSheetProcessor = uploadSheetProcessorBuilder.buildProcessor(validationLevel);
            fileRows = uploadSheetProcessor.readSheetRows(sheet);
        } catch (InvalidFormatException | InvalidOperationException | IOException e) {
            getLog().error("File: " + file.getName() + " cannot be processed", e);
            file.delete();
            throw new SheetProcessingException("File: " + file.getName() + " cannot be processed", e);
        }
    } else {
        getLog().error("File: " + file.getName() + " cannot be found");
        throw new FileNotFoundException("File does not exist");
    }
    String eRelease = ensemblRestTemplateService.getRelease();
    // Error check each row
    if (!fileRows.isEmpty()) {
        // Check for missing values and syntax errors that would prevent code creating an association
        for (AssociationUploadRow row : fileRows) {
            getLog().info("Syntax checking row: " + row.getRowNumber() + " of file, " + file.getAbsolutePath());
            RowValidationSummary rowValidationSummary = createRowValidationSummary(row, eRelease);
            // Only store summary if there is an error
            if (!rowValidationSummary.getErrors().isEmpty()) {
                rowValidationSummaries.add(rowValidationSummary);
            }
        }
        if (rowValidationSummaries.isEmpty()) {
            //Proceed to carry out full checks of values
            fileRows.forEach(row -> {
                associationSummaries.add(createAssociationSummary(row, validationLevel, eRelease));
            });
        }
    } else {
        getLog().error("Parsing file failed");
    }
    validationSummary.setAssociationSummaries(associationSummaries);
    validationSummary.setRowValidationSummaries(rowValidationSummaries);
    return validationSummary;
}

Example 5 with AssociationSummary

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

the class AssociationUploadService method saveAssociations.

private void saveAssociations(Collection<AssociationSummary> associationSummaries, Study study, SecureUser user) throws EnsemblMappingException {
    for (AssociationSummary associationSummary : associationSummaries) {
        Association newAssociation = associationSummary.getAssociation();
        // Add creation event
        associationOperationsService.createAssociationCreationEvent(newAssociation, user);
        // Save association
        associationOperationsService.saveAssociation(newAssociation, study, associationSummary.getErrors());
    // associationOperationsService.runMapping(study.getHousekeeping().getCurator(), newAssociation, user);
    }
}