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# Source code for samsifter.models.workflow

    # -*- coding: utf-8 -*-
    """Abstraction of workflows with input, tool pipeline and output.

    .. moduleauthor:: Florian Aldehoff <faldehoff@student.uni-tuebingen.de>
    """

    import sys
    import datetime
    from os.path import basename, dirname
    from os import getlogin

    """ Qt4 """
    from PyQt4.QtCore import (QObject, QFileInfo, pyqtSignal)

    """ custom libraries """
    from samsifter.gui.dialogs import BashOptions, RmaOptions
    from samsifter.models.filter_model import FilterListModel
    from samsifter.util.serialize import WorkflowSerializer
    from samsifter.util.validation import WorkflowValidator
    from samsifter.version import samsifter_version

    class Workflow(QObject):
        """Container object for workflow related data.

        Takes care of serialization and validation using specialized objects.
        """

        # signals
        changed = pyqtSignal(str, name='changed')
        list_changed = pyqtSignal(str, name='list_changed')
        input_changed = pyqtSignal(str, name='input_changed')
        output_changed = pyqtSignal(str, name='output_changed')
        validity_changed = pyqtSignal(str, name='validity_changed')

        def __init__(self, parent=None):
            """Initializ a new instance of a workflow.

            Parameters
            ----------
            parent : QObject
                Parent Qt object, defaults to None.
            """
            super(Workflow, self).__init__(parent)
            self._filename = None
            self.in_filename = None
            self.out_filename = None
            self.run_compile_stats = True
            self.run_sam2rma = False

            self.model = FilterListModel(self)
            self.model.itemChanged.connect(self.on_change)
            self.model.rowsInserted.connect(self.on_insert)
            self.model.rowsRemoved.connect(self.on_remove)

            self.validator = WorkflowValidator(self)

            self._dirty = False     # no unsaved changes at this point
            self.infile_valid = False
            self.outfile_valid = False
            self.valid = False

        def commandline(self, hyphenated=False, multiline=False, batch=False,
                        basenames=False):
            """Creates Bash-compatible commandline for entire workflow.

            Parameters
            ----------
            hyphenated : bool, optional
                Enable hyphenation of entire commandline for use within variables
                evaluated by eval command; defaults to False.
            multiline : bool, optional
                Break long lines after each individual step of the workflow to
                improve readability; defaults to False.
            batch : bool, optional
                Enable use of variables that can be evaluated within code blocks
                like for loops or functions; defaults to False.
            basenames : bool, optional
                Shorten file paths to filename only; defaults to False.

            Returns
            -------
            str
                Commandline to be run in Bash or subprocess.
            """
            if self.model is None:
                return None

            # set hyphenation character(s)
            if hyphenated:
                hyphen = "'"
            else:
                hyphen = ""

            # set newline character(s)
            if multiline:
                # use \ for bash line continuation to increase readability
                newline = hyphen + "\\\n" + hyphen
            else:
                newline = ""

            # set filenames
            if batch:
                input_str = "${input}"
                output_str = "${output}"
            else:
                if self.in_filename is None:
                    input_str = "${input}"
                else:
                    if basenames:
                        input_str = basename(self.in_filename)
                    else:
                        input_str = self.in_filename

                if self.out_filename is None:
                    output_str = "${output}"
                else:
                    if basenames:
                        output_str = basename(self.out_filename)
                    else:
                        output_str = self.out_filename

            cl = hyphen + "cat " + input_str + newline
            for item in self.model.iterate_items():
                cl += " | " + item.commandline(basenames) + newline
            cl += " > " + output_str + hyphen + "\n"

            return cl

        def to_bash(self, filename,
                    bash_options=BashOptions(),
                    rma_options=RmaOptions()):
            """Write Bash script with optional batch processing capability.

            The batch variants take filenames as arguments while the standard call
            processes only the explicitly set input file.

            Parameters
            ----------
            filename : str
                Writable path of new bash script.
            bash_options : BashOptions, optional
                Bash options object, defaults to new instance.
            rma_options : RmaOptions, optional
                SAM2RMA options object, defaults to new instance.
            """
    #        if bash_options is None:
    #            bash_options = BashOptions()
    #
    #        if rma_options is None:
    #            rma_options = RmaOptions()

            bash_params = ''
            if (
                bash_options.get_print_commands()
                and bash_options.get_stop_on_error()
            ):
                bash_params = ' -ex'
            elif bash_options.get_print_commands():
                bash_params = ' -x'
            elif bash_options.get_stop_on_error():
                bash_params = ' -e'

            bash_path = "/bin/bash"

            header = ("#!%s%s\n# SamSifter v%s workflow\n# created %s by %s\n\n"
                      % (bash_path, bash_params, samsifter_version,
                         datetime.datetime.now().strftime("%Y-%m-%d %H:%M"),
                         getlogin()))

            settings = (
                '# SAM2RMA settings\n'
                '#sam2rma_path="%s"\n'
                'sam2rma_path=`which sam2rma`\n'
                'top_percent="%.1f"\n'
                'min_score="%.1f"\n'
                'max_expected="%.2f"\n'
                'min_support_percent="%.3f"\n'
                '\n' % (rma_options.get_sam2rma_path(),
                        rma_options.get_top_percent(),
                        rma_options.get_min_score(),
                        rma_options.get_max_expected(),
                        rma_options.get_min_support_percent())
            )

            commando = "commando=%s\n" % self.commandline(
                hyphenated=True,
                multiline=True,
                batch=True,
                basenames=bash_options.get_use_basenames()
            )

            stats_switch = ""
    #        if not bash_options.get_run_compile_stats():
    #            stats_switch = "#"

            stats_command = (
                "compile_stats "
                "--prefix ${filename} "
                "--remove --verbose "
                "> ${dirname}/${filename}.sifted.csv 2>> ${log}")

            rma_switch = ""
    #        if not bash_options.get_run_sam2rma():
    #            rma_switch = "#"

            rma_command = (
                "${sam2rma_path} "
                "--minScore ${min_score} "
                "--maxExpected ${max_expected} "
                "--topPercent ${top_percent} "
                "--minSupportPercent ${min_support_percent} "
                "--in ${output} "
                "--out ${dirname} "
                "2>> ${log}"
            )

            function = (
                "# define individual job, requires filename as input\n"
                "job() {\n"
                "    %s"
                "    input=${1}\n"
                "    filename=`basename ${1}`\n"
                "    dirname=`pwd`\n"
                "    output=${filename}.sifted.sam\n"
                "    log=${filename}.sifted.log\n"
                "    eval ${commando} 2> ${log}\n"
                "    \n"
                "    # removal of temporary statistics files is optional\n"
                "    %s%s\n"
                "    # conversion into RMA files is optional\n"
                "    %s%s\n"
                "}\n"
                "# make function and variables available to subprocesses\n"
                "export -f job\n"
                "export sam2rma_path top_percent min_score max_expected min_support_percent\n"
                "\n" % (commando, stats_switch, stats_command, rma_switch,
                        rma_command)
            )

            standard_call = (
                "eval ${commando} 2> ${log}\n"
                "# removal of temporary statistics files is optional\n"
                "%s%s\n"
                "# conversion into RMA files is optional\n"
                "%s%s\n"
                "\n" % (stats_switch, stats_command, rma_switch, rma_command)
            )

            seq_call = (
                "# sequential execution, one after another\n"
                "for input in ${@}\n"
                "do\n"
                "    job ${input}\n"
                "done\n"
                "\n"
            )

            par_call = (
                "# parallel execution, one subshell per input file\n"
                "SHELL=$(type -p bash) parallel --gnu --progress job {} ::: ${@}\n"
                "\n"
            )

            summary = (
                "# create summary file for all processed files\n"
                "summarize_stats > samsifter.summary.csv\n"
                "\n"
            )

            footer = "exit\n"

            with open(filename, 'w') as f:
                # put the script together
                f.write(header)
                if bash_options.get_processing_mode() == BashOptions.SINGLE_MODE:
                    f.write(settings)
                    f.write(commando)
                    if bash_options.get_use_basenames():
                        f.write('input="%s"\n' % basename(self.in_filename))
                        f.write('output="%s"\n' % basename(self.out_filename))
                        f.write('dirname=`pwd`\n')
                    else:
                        f.write('input="%s"\n' % self.in_filename)
                        f.write('output="%s"\n' % self.out_filename)
                        f.write('dirname="%s"\n' % dirname(self.out_filename))
                    f.write('filename=`basename ${input}`\n')
                    f.write('log=${dirname}/${filename}.sifted.log\n')
                    f.write(standard_call)
                    # no summary here, compiled stats contain more information
                elif bash_options.get_processing_mode() == BashOptions.SEQUENTIAL_MODE:
                    f.write(function)
                    f.write(seq_call)
                    f.write(summary)
                elif bash_options.get_processing_mode() == BashOptions.PARALLEL_MODE:
                    f.write(settings)
                    f.write(function)
                    f.write(par_call)
                    f.write(summary)
                f.write(footer)

        def clear(self):
            """Empties the workflow from all filenames and filter steps."""
            self.set_filename(None)
            self.set_in_filename(None)
            self.set_out_filename(None)
            self.model.removeAll()
            self.set_dirty()
            self.changed.emit("workflow cleared")

        def to_xml_string(self):
            """Represent workflow as XML tree.

            Returns
            -------
            str
                Pretty XML string representing entire workflow structure.
            """
            tree = WorkflowSerializer.workflow_to_xml(self)
            xml_string = WorkflowSerializer.tree_to_str(tree, pretty=True)
            return xml_string

        def __str__(self):
            """String representation of workflow.

            Returns
            -------
            str
                Hyphenated multiline commandline to run workflow.
            """
            return self.commandline(hyphenated=False, multiline=True)

        def __repr__(self):
            """Representation of workflow for debugging purposes."""
            rep = "SamSifter v%s Workflow" % samsifter_version
            rep += "\n- filename:\t\t%s" % self._filename
            rep += "\n- input:\t\t%s" % self.in_filename
            rep += "\n- output:\t\t%s" % self.out_filename
            rep += "\n- dirty:\t\t%s" % self._dirty
            rep += repr(self.model)
            rep += "\n"
            return rep

        """ Serialization """

        @staticmethod
        def formats():
            """Lists supported file formats for saving and loading.

            Returns
            -------
            list of str
                List of file extensions with leading asterisk, eg. ``*.ssx``.
            """
            return ["*.ssx", "*.SSX"]

        def save(self, filename=None):
            """Saves file and picks filetype depending on extension.

            Note
            ----
            Currently redundant as only XML output is supported since binary output
            was dropped.

            Parameters
            ----------
            filename : str, optional
                Writable path of new workflow file.

            Returns
            -------
            bool
                True if successful, otherwise False.
            str
                Error or success message.
            """
            if filename is not None:
                self._filename = filename

            if self._filename.endswith(".ssx") or self._filename.endswith(".SSX"):
                return self.save_xml()
            else:
                return (False,
                        "Failed to save %s: wrong file extension" % filename)

        def save_xml(self):
            """Save to file using XML serialization.

            Returns
            -------
            bool
                True if successful, otherwise False.
            str
                Error or success message.
            """
            error = None
            try:
                WorkflowSerializer.serialize(self, self._filename)
            except IOError as e:
                error = "input/ouptut error - failed to save: %s" % e
                print(error, file=sys.stderr)
            except OSError as e:
                error = "OS error - failed to save: %s" % e
                print(error, file=sys.stderr)
            finally:
                if error is not None:
                    return False, error
                self._dirty = False
                return (True, "File saved to %s" % self._filename)

        def load(self, filename):
            """Load from file using XML deserialization.

            Parameters
            ----------
            filename : str, optional
                Readable path to existing workflow file.

            Returns
            -------
            bool
                True if successful, otherwise False.
            str
                Error or success message.
            """
            error = None
            try:
                WorkflowSerializer.deserialize(self, filename)
            except IOError as e:
                error = "input/output error - failed to load: %s" % e
                print(error, file=sys.stderr)
            except OSError as e:
                error = "OS error - failed to load: %s" % e
                print(error, file=sys.stderr)
            finally:
                if error is not None:
                    return False, error
                self.input_changed.emit(self.in_filename)
                self.output_changed.emit(self.out_filename)
                self.set_filename(filename)
                self._dirty = False
                message = ("Loaded workflow with %i steps from %s"
                           % (self.model.rowCount(),
                              QFileInfo(filename).fileName()))
                self.changed.emit(message)
                return True, message

        """ event handlers """

        def on_change(self, item):
            """Handle change of workflow model."""
            self.validator.validate()
            self.validity_changed.emit("test of validity change signal")
            self.set_dirty(True)

        def on_insert(self, mdlidx, start, end):
            """Handle insertion of items into workflow model."""
            self.validator.validate()
            self.set_dirty(True)

        def on_remove(self, mdlidx, start, end):
            """Handle removal of items from workflow model."""
            self.validator.validate()
            self.set_dirty(True)

        """ Getters & Setters """

        def getModel(self):
            return self.model

    #    def setModel(self, model):
    #        self.model = model

        def get_in_filename(self):
            return self.in_filename

        def set_in_filename(self, filename):
            if filename == "":
                filename = None

            if self.in_filename != filename:
                self._dirty = True
                self.in_filename = filename
                self.validator.validate()
                self.input_changed.emit(filename)
                self.changed.emit("input filename changed to %s" % filename)

        def get_out_filename(self):
            return self.out_filename

        def set_out_filename(self, filename):
            if filename == "":
                filename = None

            if self.out_filename != filename:
                self._dirty = True
                self.out_filename = filename
                self.validator.validate()
                self.output_changed.emit(filename)
                self.changed.emit("output filename changed to %s" % filename)

        def get_run_compile_stats(self):
            return self.run_compile_stats

        def set_run_compile_stats(self, button_state):
            if int(button_state) == 0:
                self.run_compile_stats = False
            elif int(button_state) == 2:
                self.run_compile_stats = True

        def get_run_sam2rma(self):
            return self.run_sam2rma

        def set_run_sam2rma(self, button_state):
            if int(button_state) == 0:
                self.run_sam2rma = False
            elif int(button_state) == 2:
                self.run_sam2rma = True

        def is_dirty(self):
            return self._dirty

        def set_dirty(self, dirty=True):
            if self._dirty != dirty:
                self._dirty = dirty
                self.changed.emit("dirty flag changed to %s" % dirty)

        def is_valid(self):
            return self.valid

        def set_valid(self, valid=True):
            if self.valid != valid:
                self.valid = valid

        def infile_is_valid(self):
            return self.infile_valid

        def set_infile_valid(self, valid=True):
            if self.infile_valid != valid:
                self.infile_valid = valid

        def outfile_is_valid(self):
            return self.outfile_valid

        def set_outfile_valid(self, valid=True):
            if self.outfile_valid != valid:
                self.outfile_valid = valid

        def get_filename(self):
            return self._filename

        def set_filename(self, filename):
            if filename == "":
                filename = None

            if self._filename != filename:
                self._dirty = True
                self._filename = filename
                self.changed.emit("filename changed to %s" % filename)

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