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# Source code for samsifter.util.serialize

    #!/usr/bin/env python3
    # -*- coding: utf-8 -*-
    """(De-)Serialization of SamSifter workflows.

    .. moduleauthor:: Florian Aldehoff (f.aldehoff@student.uni-tuebingen.de)
    """
    import sys
    import xml.etree.ElementTree as ET
    import xml.dom.minidom as minidom

    from samsifter.models.filter import FilterItem
    from samsifter.models.parameter import (
        FilterParameter, FilterThreshold, FilterFilepath, FilterSwitch
    )
    from samsifter.version import samsifter_version

    class WorkflowSerializer():
        """(De-)Serializing workflow data for permanent storage.

        Uses ElementTree and minidom libraries to write to and read from XML files.
        """

        @classmethod
        def serialize(cls, workflow, filename):
            """Serializes workflow to XML file.

            Parameters
            ----------
            workflow : Workflow
                SamSifter workflow object to be serialized.
            filename : str
                Writable path to new XML file.

            Returns
            -------
            bool
                True on success.
            """
            return cls.tree_to_file(cls.workflow_to_xml(workflow), filename)

        @classmethod
        def deserialize(cls, workflow, filename):
            """De-serializes workflow from XML file.

            Parameters
            ----------
            workflow : Workflow
                SamSifter workflow object to be deserialized.
            filename : str
                Readable path to existing XML file.

            Returns
            -------
            bool
                True on success.
            """
            return cls.workflow_from_xml(cls.tree_from_file(filename), workflow)

        @classmethod
        def tree_from_file(cls, filename):
            """Initializes element tree from XML file.

            Parameters
            ----------
            filename : str
                Readable path to existing XML file.

            Returns
            -------
            ElementTree
                Tree representation of XML file contents.
            """
            return ET.ElementTree(file=filename)

        @classmethod
        def tree_to_file(cls, tree, filename):
            """Write element tree to XML file.

            Parameters
            ----------
            tree : ElementTree
                Tree representation of workflow.
            filename : str
                Writable path to new XML file.

            Returns
            -------
            bool
                True on success.
            """
            return tree.write(filename, xml_declaration=True, encoding='UTF-8',
                              method='xml')

        @classmethod
        def workflow_to_xml(cls, workflow):
            """Generate XML tree from workflow container.

            Parameters
            ----------
            workflow : Workflow
                SamSifter workflow container object to be serialized.

            Returns
            -------
            ElementTree
                Tree representation of workflow
            None
                If workflow is unitialized.
            """
            if workflow is None:
                return None

            root = ET.Element("workflow")

            in_file = ET.SubElement(root, 'filepath')
            in_file.set('type', 'input')
            in_file.text = workflow.get_in_filename()

            out_file = ET.SubElement(root, 'filepath')
            out_file.set('type', 'output')
            out_file.text = workflow.get_out_filename()

            filters = ET.SubElement(root, 'pipeline')
            for position, fltr in enumerate(workflow.getModel().iterate_items()):
                elem = ET.SubElement(filters, 'tool')
                elem.set('index', str(position))
                elem.set('type', 'filter')
                elem.set('name', str(fltr.text()))
                elem.set('desc', str(fltr.desc))
                elem.set('command', str(fltr.command))
                elem.set('icon_path', str(fltr.icon_path))

                # store input/output restrictions
                elem.set('input_format', str(fltr.get_input_format()))
                elem.set('input_sorting', str(fltr.get_input_sorting()))
                elem.set('input_compression', str(fltr.get_input_compression()))
                elem.set('output_format', str(fltr.get_output_format()))
                elem.set('output_sorting', str(fltr.get_output_sorting()))
                elem.set('output_compression', str(fltr.get_output_compression()))

                for param in fltr.parameters:
                    sub = ET.SubElement(elem, 'parameter')
                    if isinstance(param, FilterThreshold):
                        sub.set('type', 'threshold')
                        sub.set('minimum', str(param.get_minimum()))
                        sub.set('maximum', str(param.get_maximum()))
                        sub.set('precision', str(param.get_precision()))
                        sub.set('unit', str(param.get_unit()))
                    elif isinstance(param, FilterFilepath):
                        sub.set('type', 'filepath')
                        sub.set('readable', str(param.readable))
                        sub.set('writable', str(param.writable))
                        for idx, ext in enumerate(param.get_extensions()):
                            suffix = ET.SubElement(sub, 'suffix')
                            suffix.set('extension', ext)
                            suffix.set('index', str(idx))
                    elif isinstance(param, FilterSwitch):
                        sub.set('type', 'switch')
                        for idx, opt in enumerate(param.get_options()):
                            option = ET.SubElement(sub, 'option')
                            option.set('value', str(opt))
                            option.set('index', str(idx))
                            if isinstance(opt, bool):
                                option.set('type', 'bool')
                            elif isinstance(opt, int):
                                option.set('type', 'int')
                            elif isinstance(opt, float):
                                option.set('type', 'float')
                            elif isinstance(opt, str):
                                option.set('type', 'str')
                    elif isinstance(param, FilterParameter):
                        sub.set('type', 'parameter')
                    sub.set('name', param.text)
                    sub.set('desc', param.get_description())
                    sub.set('cli_name', str(param.get_cli_name()))
                    sub.set('required', str(param.is_required()))
                    sub.set('active', str(param.is_active()))

                    # multi-type attributes (can be None, str, int, float, bool)
                    value = ET.SubElement(sub, 'value')
                    typed_value = param.get_value()
                    type_string = cls.determine_type(typed_value)
                    value.set('type', type_string)
                    value.text = str(typed_value)

                    default = ET.SubElement(sub, 'default')
                    typed_default = param.get_default()
                    type_string = cls.determine_type(typed_default)
                    default.set('type', type_string)
                    default.text = str(typed_default)

            tree = ET.ElementTree(root)
            return tree

        @classmethod
        def workflow_from_xml(cls, tree, wf):
            """Generate workflow from XML element tree.

            Parameters
            ----------
            ElementTree
                Tree representation of workflow.
            workflow : Workflow
                SamSifter workflow container object to be de-serialized into.

            Returns
            -------
            workflow : Workflow
                SamSifter workflow container object.
            None
                If tree is unitialized.
            """
            if tree is None:
                return None

            root = tree.getroot()
            wf.clear()

            # retrieve input and output filepaths
            for filepath in root.iter(tag='filepath'):
                if filepath.attrib['type'] == 'input':
                    wf.set_in_filename(filepath.text)
                if filepath.attrib['type'] == 'output':
                    wf.set_out_filename(filepath.text)

            # retrieve filter pipeline
            for pipeline in root.iter(tag='pipeline'):
                for tool in pipeline.iter(tag='tool'):
                    text = cls.singletons(tool.get('name'))
                    desc = cls.singletons(tool.get('desc'))
                    command = cls.singletons(tool.get('command'))
                    icon_path = cls.singletons(tool.get('icon_path'))

                    # retrieve input and output restrictions
                    input_format = cls.singletons(tool.get('input_format'))
                    input_sorting = cls.singletons(tool.get('input_sorting'))
                    input_compression = cls.singletons(
                        tool.get('input_compression'))
                    output_format = cls.singletons(tool.get('output_format'))
                    output_sorting = cls.singletons(tool.get('output_sorting'))
                    output_compression = cls.singletons(
                        tool.get('output_compression'))

                    item = FilterItem(text, desc, icon_path)
                    item.set_command(command)
                    item.set_input_format(input_format)
                    item.set_input_sorting(input_sorting)
                    item.set_input_compression(input_compression)
                    item.set_output_format(output_format)
                    item.set_output_sorting(output_sorting)
                    item.set_output_compression(output_compression)

                    for param in tool.iter(tag='parameter'):
                        param_name = param.get('name')
                        param_desc = param.get('desc')
                        cli_name = param.get('cli_name')
                        required = cls.singletons(param.get('required'))
                        active = cls.singletons(param.get('active'))

                        # retrieve value and desc, cast according to type
                        for val in param.iter(tag='value'):
                            val_type = val.get('type')
                            if val_type == 'None':
                                value = cls.singletons(val.text)
                            elif val_type == 'bool':
                                value = cls.singletons(val.text)
                            elif val_type == 'int':
                                value = int(cls.singletons(val.text))
                            elif val_type == 'float':
                                value = float(cls.singletons(val.text))
                            elif val_type == 'str':
                                value = str(cls.singletons(val.text))

                        for dflt in param.iter(tag='default'):
                            dflt_type = dflt.get('type')
                            if dflt_type == 'None':
                                default = cls.singletons(dflt.text)
                            elif dflt_type == 'bool':
                                default = cls.singletons(dflt.text)
                            elif dflt_type == 'int':
                                default = int(cls.singletons(dflt.text))
                            elif dflt_type == 'float':
                                default = float(cls.singletons(dflt.text))
                            elif dflt_type == 'str':
                                default = str(cls.singletons(dflt.text))

                        # check for parameter type, initialise subclasses
                        param_type = param.get('type')
                        parameter = None
                        if param_type == 'threshold':
                            minimum = float(cls.singletons(param.get('minimum')))
                            maximum = float(cls.singletons(param.get('maximum')))
                            precision = int(cls.singletons(param.get('precision')))
                            unit = cls.singletons(param.get('unit'))

                            parameter = FilterThreshold(
                                param_name, param_desc, cli_name, default, minimum,
                                maximum, precision, unit, value, required, active
                            )
                        elif param_type == 'filepath':
                            readable = cls.singletons(param.get('readable'))
                            writable = cls.singletons(param.get('writable'))
                            extensions = []
                            for sffx in param.iter('suffix'):
                                extensions.append(cls.singletons(
                                                  sffx.get('extension')))
                            if len(extensions) <= 0:
                                extensions = None

                            parameter = FilterFilepath(
                                param_name, param_desc, cli_name, default,
                                extensions, readable, writable, value, required,
                                active
                            )
                        elif param_type == 'switch':
                            options = []
                            for choice in param.iter(tag='option'):
                                opt_type = choice.get('type')
                                if opt_type == 'None':
                                    option = cls.singletons(choice.get('value'))
                                elif opt_type == 'bool':
                                    option = cls.singletons(choice.get('value'))
                                elif opt_type == 'int':
                                    option = int(cls.singletons(
                                                 choice.get('value')))
                                elif opt_type == 'float':
                                    option = float(cls.singletons(
                                                   choice.get('value')))
                                elif opt_type == 'str':
                                    option = cls.singletons(choice.get('value'))
                                options.append(option)

                            if len(options) <= 0:
                                options = None

                            parameter = FilterSwitch(
                                param_name, param_desc, cli_name, default, options,
                                value, required, active
                            )
                        elif param_type == 'parameter':
                            # no special parameters for this base class
                            parameter = FilterParameter(
                                param_name, param_desc, cli_name, default, value,
                                required, active
                            )
                        else:
                            print("failed to determine parameter type",
                                  file=sys.stderr)
                            continue

                        item.add_parameter(parameter)
                    wf.getModel().insertItem(item)
            return wf

        @classmethod
        def singletons(cls, value):
            """Replaces 'None', 'False' and 'True' strings with actual singletons.

            Helper method for deserialization from strings to actual Python
            singleton entities.

            Parameters
            ----------
            value : str
                Value string from XML file.

            Returns
            -------
            None
                If string represents None.
            bool
                If string represents True or False.
            str
                If string does not represent a singleton.
            """
            if value == 'None':
                return None
            elif value == 'False':
                return False
            elif value == 'True':
                return True
            else:
                return value

        @classmethod
        def determine_type(cls, value):
            """Determines type of a typed value and return it as string.

            Helper method for serialization of typed Python values to string
            representations in XML.

            Parameters
            ----------
            value : bool, str, int, float
                Typed value.

            Returns
            -------
            str
                String representation of value type.
            """
            if value is None:
                return 'None'
            elif isinstance(value, str):
                return 'str'
            elif isinstance(value, bool):
                return 'bool'
            elif isinstance(value, int):
                return 'int'
            elif isinstance(value, float):
                return 'float'
            else:
                return 'str'

        @classmethod
        def prettify(cls, elem, indent="  "):
            """Create a pretty-printed XML string for an individual tree element.

            Parameters
            ----------
            elem : Element
                Tree element.
            indent : str, optional
                Indentation character(s) to distinguish tree levels, defaults to
                doublespace.

            Returns
            -------
            str
                Pretty XML string representing the element.
            """
            rough_string = ET.tostring(elem, encoding='UTF-8', method='xml')
            reparsed = minidom.parseString(rough_string)
            return reparsed.toprettyxml(indent)

        @classmethod
        def tree_to_str(cls, tree, pretty=False):
            """Converts XML element tree to optionally indented text string.

            Parameters
            ----------
            tree : ElementTree
                Tree to be printed.
            pretty : bool, optional
                Enable indentation and multiline string representation for better
                legibility of the XML, default to False.

            Returns
            -------
            str
                XML string representing the tree.
            """
            root = tree.getroot()
            if pretty:
                return WorkflowSerializer.prettify(root)
            else:
                return ET.tostring(root, encoding='UTF-8', method='xml')

    def main(argv):
        """Simple test of workflow serialization and deserialization."""
        outfilename = "/home/aldehoff/sandbox/serial_test.xml"
    #    infilename = "/home/aldehoff/sandbox/serial_test_modified.xml"
        infilename = "/home/aldehoff/sandbox/serial_test2.xml"

        from samsifter.util.testing import create_workflow
        workflow = create_workflow()

        # serialization
        WorkflowSerializer.serialize(workflow, outfilename)

        print("*" * 40)

        # deserialization
        WorkflowSerializer.deserialize(workflow, infilename)
        workflow.set_filename(infilename)

        # inspection of workflow for changes (filename should be in another dir)
        print(repr(workflow))

        exit()

    if __name__ == '__main__':
        main(sys.argv)

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