multielectrode_grasp/code/python-odml/odml/scripts/odml_to_rdf.py

"""odmlToRDF

odmlToRDF searches for odML files within a provided SEARCHDIR
and converts them to the newest odML format version and
exports all found and resulting odML files to XML formatted RDF.
Original files will never be overwritten. New files will be
written either to a new directory at the current or a specified
location.

Usage: odmltordf [-r] [-o OUT] SEARCHDIR

Arguments:
    SEARCHDIR       Directory to search for odML files.

Options:
    -o OUT          Output directory. Must exist if specified.
                    If not specified, output files will be
                    written to the current directory.
    -r              Search recursively. Directory structures
                    will not be retained.
    -h --help       Show this screen.
    --version       Show version.
"""

import os
import pathlib
import sys
import tempfile

from docopt import docopt

try:
    from StringIO import StringIO
except ImportError:
    from io import StringIO

import odml

from odml.tools.odmlparser import ODMLReader, ODMLWriter
from odml.tools.version_converter import VersionConverter as VerConf

try:
    unicode = unicode
except NameError:
    unicode = str


def run_rdf_export(odml_file, export_dir):
    """
    Convert an odML file to an XML RDF file and
    export it to an export directory with the
    same name as the original file and a '.rdf' file
    ending.
    :param odml_file: odML file to be converted to RDF.
    :param export_dir:
    """
    out_name = os.path.splitext(os.path.basename(odml_file))[0]
    out_file = os.path.join(export_dir, "%s.rdf" % out_name)
    doc = ODMLReader().from_file(odml_file)
    ODMLWriter("RDF").write_file(doc, out_file)


def run_conversion(file_list, output_dir, rdf_dir, report, source_format="XML"):
    """
    Convert a list of odML files to the latest odML version if required
    and export all files to XML RDF files in a specified output directory.
    :param file_list: list of files to be exported to RDF.
    :param output_dir: Directory where odML files converted to
                       the latest odML version will be saved.
    :param rdf_dir: Directory where exported RDF files will be saved.
    :param report: Reporting StringIO.
    :param source_format: Original file format of the odML source files.
                          XML, JSON and YAML are supported, default is XML.
    """
    # Exceptions are kept as broad as possible to ignore any non-odML or
    # invalid odML files and ensuring everything that can be will be converted.
    for curr_file in file_list:
        file_path = unicode(curr_file.absolute())
        report.write("[Info] Handling file '%s'\n" % file_path)
        # When loading the current file succeeds, it is
        # a recent odML format file and can be exported
        # to RDF right away. Otherwise it needs to be
        # converted to the latest odML version first.
        try:
            odml.load(file_path, source_format)
            report.write("[Info] RDF conversion of '%s'\n" % file_path)
            run_rdf_export(file_path, rdf_dir)
        except Exception as exc:
            out_name = os.path.splitext(os.path.basename(file_path))[0]
            outfile = os.path.join(output_dir, "%s_conv.xml" % out_name)
            try:
                VerConf(file_path).write_to_file(outfile, source_format)
                try:
                    report.write("[Info] RDF conversion of '%s'\n" % outfile)
                    run_rdf_export(outfile, rdf_dir)
                except Exception as exc:
                    report.write("[Error] converting '%s' to RDF: '%s'\n" %
                                 (file_path, exc))
            except Exception as exc:
                # Ignore files we cannot parse or convert
                report.write("[Error] version converting file '%s': '%s'\n" %
                             (file_path, exc))


def main(args=None):
    """
    Convenience script to automatically convert odML files
    within a directory (tree) to RDF. Check the cli help
    for details.
    :param args: Command line arguments
    """
    parser = docopt(__doc__, argv=args, version="0.1.0")

    root = parser['SEARCHDIR']
    if not os.path.isdir(root):
        print(docopt(__doc__, "-h"))
        exit(1)

    # Handle all supported odML file formats.
    if parser['-r']:
        xfiles = list(pathlib.Path(root).rglob('*.odml'))
        xfiles.extend(list(pathlib.Path(root).rglob('*.xml')))
        jfiles = list(pathlib.Path(root).rglob('*.json'))
        yfiles = list(pathlib.Path(root).rglob('*.yaml'))
    else:
        xfiles = list(pathlib.Path(root).glob('*.odml'))
        xfiles.extend(list(pathlib.Path(root).glob('*.xml')))
        jfiles = list(pathlib.Path(root).glob('*.json'))
        yfiles = list(pathlib.Path(root).glob('*.yaml'))

    out_root = os.getcwd()
    if parser["-o"]:
        if not os.path.isdir(parser["-o"]):
            print("[Error] Could not find output directory '%s'" % parser["-o"])
            exit(1)

        out_root = parser["-o"]

    out_dir = tempfile.mkdtemp(prefix="odmlconv_", dir=out_root)
    rdf_dir = tempfile.mkdtemp(prefix="odmlrdf_", dir=out_dir)

    # Use this monkeypatch reporter until there is a way
    # to run the converters silently.
    report = StringIO()
    report.write("[Info] Files will be saved to '%s'\n" % out_dir)

    run_conversion(xfiles, out_dir, rdf_dir, report)
    run_conversion(jfiles, out_dir, rdf_dir, report, "JSON")
    run_conversion(yfiles, out_dir, rdf_dir, report, "YAML")

    print(report.getvalue())
    report.close()


if __name__ == "__main__":
    main(sys.argv[1:])