nl.uu.cs.ape.configuration.APEConfigException Maven / Gradle / Ivy

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APE is a command line tool and an API for the automated exploration of possible computational pipelines (workflows) from large collections of computational tools.
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package nl.uu.cs.ape.configuration;

import org.json.JSONObject;

import nl.uu.cs.ape.configuration.tags.validation.ValidationResults;

/**
 * This {@link APEConfigException} will be thrown if the configuration is
 * incorrect.
 * Additional info will be provided to help the user fix the problem.
 * The static methods in this class can also be used to throw other kinds of
 * exceptions regarding the core- and run configuration.
 * 
 * The configuration problems can be classified in three exceptions:
 * 

 * APEConfigException: Application specific configuration exceptions.
 * JSONException: Values or files that cannot be parsed to a value.
 * IOException: Errors in in reading from the file system.
 * 
 */
public class APEConfigException extends RuntimeException {

    /**
     * Instantiates a new Ape config exception.
     *
     * @param message The message that will be passed to the {@link Exception} super
     *                class.
     */
    public APEConfigException(String message) {
        super(message);
    }

    /**
     * Invalid value ape config exception.
     *
     * @param tag   Corresponding JSON tag in the configuration file.
     * @param value The value for the tag, provided by the user.
     * @param info  Application specific information that may help the user solve
     *              the problem.
     * @return Configuration exception with information that may help the user solve
     *         the problem.
     */
    public static APEConfigException invalidValue(String tag, Object value, String info) {
        return new APEConfigException(String.format("'%s' is not a valid value for tag '%s', %s", value, tag, info));
    }

    /**
     * Invalid value ape config exception.
     *
     * @param tag    Corresponding JSON tag in the configuration file.
     * @param config The configuration provided by the user.
     * @param info   Application specific information that may help the user solve
     *               the problem.
     * @return Configuration exception with information that may help the user solve
     *         the problem.
     */
    public static APEConfigException invalidValue(String tag, JSONObject config, String info) {
        return new APEConfigException(
                String.format("'%s' is not a valid value for tag '%s', %s", config.get(tag), tag, info));
    }

    /**
     * Missing tag ape config exception.
     *
     * @param tag Corresponding JSON tag in the configuration file.
     * @return Configuration exception with information that may help the user solve
     *         the problem.
     */
    public static APEConfigException missingTag(String tag) {
        return new APEConfigException(String.format("Tag '%s' is not provided, cannot setup the configuration.", tag));
    }

    /**
     * Cannot parse ape config exception.
     *
     * @param           The type that APE cannot parse to.
     * @param tag          Corresponding JSON tag in the configuration file.
     * @param value        The value for the tag, provided by the user.
     * @param expectedType The type that APE cannot parse to.
     * @param info         Application specific information that may help the user
     *                     solve the problem.
     * @return Configuration exception with information that may help the user solve
     *         the problem.
     */
    public static  APEConfigException cannotParse(String tag, Object value, Class expectedType, String info) {
        return new APEConfigException(String.format("Value '%s' cannot be parsed to type '%s' for tag '%s', %s", value,
                expectedType.getSimpleName(), tag, info));
    }

    /**
     * Required validation tag json exception.
     *
     * @param tag         the tag
     * @param requiredTag the required tag
     * @param info        the info
     * @return the json exception
     */
    public static APEConfigException requiredValidationTag(String tag, String requiredTag, String info) {
        return new APEConfigException(String.format("Cannot parse tag '%s' without '%s', %s", tag, requiredTag, info));
    }

    /**
     * Path not found ape config exception.
     *
     * @param tag  Corresponding JSON tag in the configuration file.
     * @param path The relative- or absolute path to a JSON- or OWL file.
     * @return Configuration exception with information that may help the user solve
     *         the problem.
     */
    public static APEConfigException pathNotFound(String tag, String path) {
        return new APEConfigException(String.format("Provided path '%s' for tag '%s' does not exist.", path, tag));
    }

    /**
     * Path is found, but it is not a file.
     *
     * @param tag  Corresponding JSON tag in the configuration file.
     * @param path The relative- or absolute path to a JSON- or OWL file.
     * @return Configuration exception with information that may help the user solve
     *         the problem.
     */
    public static APEConfigException notAFile(String tag, String path) {
        return new APEConfigException(String.format("Provided path '%s' for tag '%s' is not a file.", path, tag));
    }

    /**
     * Path is found, but it is not a directory.
     *
     * @param tag  Corresponding JSON tag in the configuration file.
     * @param path The relative- or absolute path to a JSON- or OWL file.
     * @return Configuration exception with information that may help the user solve
     *         the problem.
     */
    public static APEConfigException notADirectory(String tag, String path) {
        return new APEConfigException(String.format("Provided path '%s' for tag '%s' is not a directory.", path, tag));
    }

    /**
     * Missing permission ape config exception.
     *
     * @param tag               Corresponding JSON tag in the configuration file.
     * @param path              The relative- or absolute path to a JSON- or OWL
     *                          file.
     * @param missingPermission The missing READ or WRITE permission for the file
     *                          described by the path.
     * @return Configuration exception with information that may help the user solve
     *         the problem.
     */
    public static APEConfigException missingPermission(String tag, String path, Object missingPermission) {
        return new APEConfigException(String.format("You are missing [%s] permission for path '%s' for tag '%s'",
                missingPermission, path, tag));
    }

    /**
     * List all the failed validation criteria in one exception.
     *
     * @param validationResults the validation results
     * @return the json exception
     */
    public static APEConfigException ruleViolations(ValidationResults validationResults) {
        StringBuilder sb = new StringBuilder();
        validationResults.getFails().forEach(fail -> sb
                .append(String.format("Tag '%s' is incorrect: %s%n", fail.getTag(), fail.getRuleDescription())));
        return new APEConfigException(sb.toString());
    }

    /**
     * The annotated type (workflow input or output) is not defined within the
     * domain taxonomy.
     *
     * @param typeID - ID of the data type not defined
     * @return Run configuration exception with information that may help the user
     *         solve the problem.
     */
    public static APEConfigException workflowIODataTypeNotInDomain(String typeID) {
        return new APEConfigException(String.format(
                "Data type '%s'used to annotate workflow input/output is not defined in the taxonomy.", typeID));
    }
}