# ############################################################################ #

import os, sys


from amanzi import input_tree

# ############################################################################ #


class AmanziDataOutput:

    CYCLE_REGEX_PATTERN = r".h5.(\d+).xmf"
    XMF_TIME_TAG = "Time"
    XMF_TIME_VALUE_ATTR = "Value"
    XMF_DATASET_TAG = "Attribute"
    XMF_DATASET_NAME_ATTR = "Name"

    def __init__(self, xmf_filename, directory=None):

        from xml.etree import ElementTree as ETree
        import re

        # Set to current directory if not set
        try:
            self.output_dir = os.path.abspath(directory)
        except Exception:
            self.output_dir = os.getcwd()

        # Set filename to the full path
        self.filename = os.path.abspath(
            self.output_dir + os.sep + xmf_filename
        )

        # Define the cycle
        base_file = os.path.basename(self.filename)
        self.cycle = int(
            re.search(self.CYCLE_REGEX_PATTERN, base_file).group(1)
        )

        # Search for the XMF file need to open it with ElementTree
        try:
            tree = ETree.parse(self.filename)
        except IOError:
            print("Failed to open:" + self.filename)
            raise
        except Exception:
            raise

        # Find the time
        time_elem = tree.getiterator(tag=self.XMF_TIME_TAG)[0]
        self.time = float(time_elem.get(self.XMF_TIME_VALUE_ATTR))

        # Now find all the datasets
        self.datasets = []
        dataset_iter = tree.getiterator(tag=self.XMF_DATASET_TAG)
        for elem in tree.getiterator(tag=self.XMF_DATASET_TAG):
            self.datasets.append(elem.get(self.XMF_DATASET_NAME_ATTR))


class AmanziInterface:

    AMANZI_CHECKPOINT_REGEX = r"checkpoint\d+.h5"
    AMANZI_DATAFILE_REGEX = r"_data.h5"

    def __init__(
        self,
        binary=None,
        input=None,
        output=None,
        error=None,
        mpiexec="mpiexec",
    ):

        self.binary = binary
        self.mpiexec = mpiexec
        self.input = input
        self.output = output
        self.error = error

        self.nprocs = 0
        self.exit_code = None
        self.args = []

        self.data_files = []

    def run(self):
        import time
        import signal

        try:
            import subprocess
        except ImportError:
            print("Failed to import module subprocess")
            print("Module is avail in Python 2.4 and higher")
            print("Current Python version " + str(sys.version))
            raise
        except Exception:
            print("Unknown error:", sys.exc_info())
            raise

        # Check the files
        if not self._check_binary():
            raise ValueError("Can not run binary")

        if not self._check_input():
            raise ValueError("Invalid input")

        if self.nprocs > 0:
            if not self._check_mpiexec:
                raise ValueError("Can not launch a parallel executable")

        # Open files to redirect STDOUT and STDERR
        try:
            stdout_fh = open(self.output, "w")
        except (ValueError, TypeError):
            stdout_fh = None
        except IOError:
            raise IOError("Failed to open " + self.output)
        except:
            print("Unknown exception:", sys.exc_info()[0])
            raise

        try:
            stderr_fh = open(self.error, "w")
        except (ValueError, TypeError):
            stderr_fh = None
        except IOError:
            raise IOError("Failed to open " + self.error)
        except:
            print("Unknown exception")
            raise

        # Define the arguments and execuables
        if self.nprocs == 0:
            executable = self.binary
            args = [executable, self.input_option()]
        else:
            executable = self.mpiexec
            args = [
                executable,
                "-n",
                str(self.nprocs),
                self.binary,
                self.input_option(),
            ]

        # Open a pipe, catch a CTRL-C shut down the pipe
        try:
            pipe = subprocess.Popen(
                args,
                executable=executable,
                bufsize=-1,
                stdout=stdout_fh,
                stderr=stderr_fh,
            )
        except ValueError:
            raise ValueError("Popen called with incorrect arguments")
        except OSError:
            print("Failed to run " + str(args))
            raise OSError("Failed to run Amanzi binary " + self.binary)
        else:
            try:
                pipe.wait()
            except KeyboardInterrupt:
                try:
                    kill_signal = signal.SIGKILL
                except AttributeError:
                    kill_signal = signal.SIGTERM
                    print("Sending SIGTERM to Amanzi run PID=" + str(pipe.pid))
                    os.kill(pipe.pid, signal.SIGTERM)
                    time.sleep(1)
                    while pipe.poll() is None:
                        print(
                            "PID="
                            + str(pipe, pipe.pid)
                            + " still alive. Sending signal (SIGKILL) "
                            + str(kill_signal)
                        )
                        os.kill(pipe.pid, kill_signal)
                        time.sleep(5)

        # Set the return code
        self.exit_code = pipe.returncode

        # Flush and close the files
        try:
            stdout_fh.flush()
        except:
            pass
        else:
            stdout_fh.close()

        try:
            stderr_fh.flush()
        except:
            pass
        else:
            stderr_fh.close()

        return pipe.returncode

    def input_option(self):
        return "--xml_file=" + self.input

    def _check_mpiexec(self):
        from os import path, access, R_OK, X_OK

        try:
            exists = os.path.exists(self.mpiexec)
        except TypeError:
            print("MPI launch command is not defined")
            raise

        ok_flag = False
        if (
            exists
            and path.isfile(self.mpiexec)
            and access(self.mpiexec, R_OK | X_OK)
        ):
            ok_flag = True
        else:
            print(
                amanzi.mpiexec
                + " does not exist or is not readable or is not executable"
            )

        return ok_flag

    def _check_binary(self):
        from os import path, access, R_OK, X_OK

        try:
            exists = os.path.exists(self.binary)
        except TypeError:
            print("Amanzi binary is not defined")
            raise

        ok_flag = False
        if (
            exists
            and path.isfile(self.binary)
            and access(self.binary, R_OK | X_OK)
        ):
            ok_flag = True
        else:
            print(self.binary + " does not exist or is not readable")

        return ok_flag

    def _check_input(self):
        from os import path, access, R_OK

        try:
            exists = os.path.exists(self.input)
        except TypeError:
            print("Input file is not defined")
            raise

        ok_flag = False
        if exists and path.isfile(self.input) and access(self.input, R_OK):
            ok_flag = True
        else:
            print(amanzi.input + " does not exist or is not readable")

        return ok_flag

    def find_data_files(self, basename, directory=None):
        import glob

        try:
            output_xmf_regex = basename + "_data.h5" + ".[0-9]*" + ".xmf"
        except Exception:
            print("Failed to build XMF output regular expression pattern")
            raise

        try:
            output_xmf_regex = directory + os.sep + output_xmf_regex
        except Exception:
            pass

        print("output_xmf_regex=" + output_xmf_regex)

        for output in glob.glob(output_xmf_regex):
            print("File=" + output)
            self.data_files.append(AmanziDataOutput(output))

        return self.data_files

    def sort_data_files(self, files=[]):
        if len(files) == 0:
            if len(self.data_files) == 0:
                basename = self.plot_output_basename()
                self.find_data_files(basename)
            files = self.data_files

        search_dict = {}
        for data_file in files:
            search_dict[data_file.cycle] = data_file

        sorted_cycles = search_dict.keys()
        sorted_cycles.sort()
        sorted_files = []
        for n in sorted_cycles:
            sorted_files.append(search_dict.get(n))

        return sorted_files

    def find_mesh_file(self, input=None):
        import glob

        basename = self.plot_output_basename(input)

        mesh_regex = basename + "_mesh.h5"
        try:
            mesh_file = glob.glob(mesh_regex)[0]
        except Exception:
            print(
                "Could not find mesh file matching '"
                + mesh_regex
                + "' pattern"
            )
            mesh_file = None

        return mesh_file

    def plot_output_basename(self, input=None):

        from amanzi.trilinos import InputList as AmanziInput

        if input is None:
            input_tree = AmanziInput(self.input)
        else:
            input_tree = AmanziInput(input)

        output_ctrl = input_tree.find_sublist("Output")
        viz_ctrl = output_ctrl.find_sublist("Visualization Data")

        return viz_ctrl.find_parameter("File Name Base").get_value()


if __name__ == "__main__":

    try:
        amanzi = AmanziInterface("duh.xml")
    except ValueError:
        print("Caught the invalid input error")

# ############################################################################ #

import os, sys


from amanzi import input_tree

# ############################################################################ #


class AmanziDataOutput:

    CYCLE_REGEX_PATTERN = r".h5.(\d+).xmf"
    XMF_TIME_TAG = "Time"
    XMF_TIME_VALUE_ATTR = "Value"
    XMF_DATASET_TAG = "Attribute"
    XMF_DATASET_NAME_ATTR = "Name"

    def __init__(self, xmf_filename, directory=None):

        from xml.etree import ElementTree as ETree
        import re

        # Set to current directory if not set
        try:
            self.output_dir = os.path.abspath(directory)
        except Exception:
            self.output_dir = os.getcwd()

        # Set filename to the full path
        self.filename = os.path.abspath(
            self.output_dir + os.sep + xmf_filename
        )

        # Define the cycle
        base_file = os.path.basename(self.filename)
        self.cycle = int(
            re.search(self.CYCLE_REGEX_PATTERN, base_file).group(1)
        )

        # Search for the XMF file need to open it with ElementTree
        try:
            tree = ETree.parse(self.filename)
        except IOError:
            print("Failed to open:" + self.filename)
            raise
        except Exception:
            raise

        # Find the time
        time_elem = tree.getiterator(tag=self.XMF_TIME_TAG)[0]
        self.time = float(time_elem.get(self.XMF_TIME_VALUE_ATTR))

        # Now find all the datasets
        self.datasets = []
        dataset_iter = tree.getiterator(tag=self.XMF_DATASET_TAG)
        for elem in tree.getiterator(tag=self.XMF_DATASET_TAG):
            self.datasets.append(elem.get(self.XMF_DATASET_NAME_ATTR))


class AmanziInterface:

    AMANZI_CHECKPOINT_REGEX = r"checkpoint\d+.h5"
    AMANZI_DATAFILE_REGEX = r"_data.h5"

    def __init__(
        self,
        binary=None,
        input=None,
        output=None,
        error=None,
        mpiexec="mpiexec",
    ):

        self.binary = binary
        self.mpiexec = mpiexec
        self.input = input
        self.output = output
        self.error = error

        self.nprocs = 0
        self.exit_code = None
        self.args = []

        self.data_files = []

    def run(self):
        import time
        import signal

        try:
            import subprocess
        except ImportError:
            print("Failed to import module subprocess")
            print("Module is avail in Python 2.4 and higher")
            print("Current Python version " + str(sys.version))
            raise
        except Exception:
            print("Unknown error:", sys.exc_info())
            raise

        # Check the files
        if not self._check_binary():
            raise ValueError("Can not run binary")

        if not self._check_input():
            raise ValueError("Invalid input")

        if self.nprocs > 0:
            if not self._check_mpiexec:
                raise ValueError("Can not launch a parallel executable")

        # Open files to redirect STDOUT and STDERR
        try:
            stdout_fh = open(self.output, "w")
        except (ValueError, TypeError):
            stdout_fh = None
        except IOError:
            raise IOError("Failed to open " + self.output)
        except:
            print("Unknown exception:", sys.exc_info()[0])
            raise

        try:
            stderr_fh = open(self.error, "w")
        except (ValueError, TypeError):
            stderr_fh = None
        except IOError:
            raise IOError("Failed to open " + self.error)
        except:
            print("Unknown exception")
            raise

        # Define the arguments and execuables
        if self.nprocs == 0:
            executable = self.binary
            args = [executable, self.input_option()]
        else:
            executable = self.mpiexec
            args = [
                executable,
                "-n",
                str(self.nprocs),
                self.binary,
                self.input_option(),
            ]

        # Open a pipe, catch a CTRL-C shut down the pipe
        try:
            pipe = subprocess.Popen(
                args,
                executable=executable,
                bufsize=-1,
                stdout=stdout_fh,
                stderr=stderr_fh,
            )
        except ValueError:
            raise ValueError("Popen called with incorrect arguments")
        except OSError:
            print("Failed to run " + str(args))
            raise OSError("Failed to run Amanzi binary " + self.binary)
        else:
            try:
                pipe.wait()
            except KeyboardInterrupt:
                try:
                    kill_signal = signal.SIGKILL
                except AttributeError:
                    kill_signal = signal.SIGTERM
                    print("Sending SIGTERM to Amanzi run PID=" + str(pipe.pid))
                    os.kill(pipe.pid, signal.SIGTERM)
                    time.sleep(1)
                    while pipe.poll() is None:
                        print(
                            "PID="
                            + str(pipe, pipe.pid)
                            + " still alive. Sending signal (SIGKILL) "
                            + str(kill_signal)
                        )
                        os.kill(pipe.pid, kill_signal)
                        time.sleep(5)

        # Set the return code
        self.exit_code = pipe.returncode

        # Flush and close the files
        try:
            stdout_fh.flush()
        except:
            pass
        else:
            stdout_fh.close()

        try:
            stderr_fh.flush()
        except:
            pass
        else:
            stderr_fh.close()

        return pipe.returncode

    def input_option(self):
        return "--xml_file=" + self.input

    def _check_mpiexec(self):
        from os import path, access, R_OK, X_OK

        try:
            exists = os.path.exists(self.mpiexec)
        except TypeError:
            print("MPI launch command is not defined")
            raise

        ok_flag = False
        if (
            exists
            and path.isfile(self.mpiexec)
            and access(self.mpiexec, R_OK | X_OK)
        ):
            ok_flag = True
        else:
            print(
                amanzi.mpiexec
                + " does not exist or is not readable or is not executable"
            )

        return ok_flag

    def _check_binary(self):
        from os import path, access, R_OK, X_OK

        try:
            exists = os.path.exists(self.binary)
        except TypeError:
            print("Amanzi binary is not defined")
            raise

        ok_flag = False
        if (
            exists
            and path.isfile(self.binary)
            and access(self.binary, R_OK | X_OK)
        ):
            ok_flag = True
        else:
            print(self.binary + " does not exist or is not readable")

        return ok_flag

    def _check_input(self):
        from os import path, access, R_OK

        try:
            exists = os.path.exists(self.input)
        except TypeError:
            print("Input file is not defined")
            raise

        ok_flag = False
        if exists and path.isfile(self.input) and access(self.input, R_OK):
            ok_flag = True
        else:
            print(amanzi.input + " does not exist or is not readable")

        return ok_flag

    def find_data_files(self, basename, directory=None):
        import glob

        try:
            output_xmf_regex = basename + "_data.h5" + ".[0-9]*" + ".xmf"
        except Exception:
            print("Failed to build XMF output regular expression pattern")
            raise

        try:
            output_xmf_regex = directory + os.sep + output_xmf_regex
        except Exception:
            pass

        print("output_xmf_regex=" + output_xmf_regex)

        for output in glob.glob(output_xmf_regex):
            print("File=" + output)
            self.data_files.append(AmanziDataOutput(output))

        return self.data_files

    def sort_data_files(self, files=[]):
        if len(files) == 0:
            if len(self.data_files) == 0:
                basename = self.plot_output_basename()
                self.find_data_files(basename)
            files = self.data_files

        search_dict = {}
        for data_file in files:
            search_dict[data_file.cycle] = data_file

        sorted_cycles = search_dict.keys()
        sorted_cycles.sort()
        sorted_files = []
        for n in sorted_cycles:
            sorted_files.append(search_dict.get(n))

        return sorted_files

    def find_mesh_file(self, input=None):
        import glob

        basename = self.plot_output_basename(input)

        mesh_regex = basename + "_mesh.h5"
        try:
            mesh_file = glob.glob(mesh_regex)[0]
        except Exception:
            print(
                "Could not find mesh file matching '"
                + mesh_regex
                + "' pattern"
            )
            mesh_file = None

        return mesh_file

    def plot_output_basename(self, input=None):

        from amanzi.trilinos import InputList as AmanziInput

        if input is None:
            input_tree = AmanziInput(self.input)
        else:
            input_tree = AmanziInput(input)

        output_ctrl = input_tree.find_sublist("Output")
        viz_ctrl = output_ctrl.find_sublist("Visualization Data")

        return viz_ctrl.find_parameter("File Name Base").get_value()


if __name__ == "__main__":

    try:
        amanzi = AmanziInterface("duh.xml")
    except ValueError:
        print("Caught the invalid input error")

# ############################################################################ # # ############################################################################ # # Set to current directory if not set # Set filename to the full path # Define the cycle # Search for the XMF file need to open it with ElementTree # Find the time # Now find all the datasets # Check the files # Open files to redirect STDOUT and STDERR # Define the arguments and execuables # Open a pipe, catch a CTRL-C shut down the pipe # Set the return code # Flush and close the files