root/spongenet/trunk/spongenet/parse.py

#!/usr/bin/env python

"""
Parse combined sponge data XML files.

Usage:

   > python parse.py path/to/xml/file
   > python parse.py -t
   > python parse.py --test

Test silent import.

>>> import parse
"""

__author__ = "Chris Calloway"
__email__ = "cbc@chriscalloway.org"
__copyright__ = "Copyright 2010 UNC-CH Department of Marine Science"
__license__ = "GPL2"

import sys
import os
import glob
import hashlib
import doctest
import unittest
from StringIO import StringIO
import xml.etree.ElementTree as ET

USAGE = "\n".join(__doc__.splitlines()[3:8])
TEST_PATH = os.path.join("tests", "parse")


def _test():
    """
    Run doctests as unittest suite.

    Test silent import

    >>> from parse import _test
    """

    suite = []
    suite.append(doctest.DocTestSuite())
    suite = unittest.TestSuite(suite)
    unittest.TextTestRunner().run(suite)

    return


def xmldoc_path():
    """
    Return the XML document file path from the command line.

    Supply too few arguments on command line.

    >>> save_stdout = sys.stdout
    >>> temp_stdout = StringIO()
    >>> sys.stdout = temp_stdout
    >>> sys.argv = []
    >>> _xmldoc_path = xmldoc_path()
    >>> sys.stdout = save_stdout
    >>> USAGE == temp_stdout.getvalue()[:-1]
    True

    Supply too many arguments on the command line.

    >>> save_stdout = sys.stdout
    >>> temp_stdout = StringIO()
    >>> sys.stdout = temp_stdout
    >>> sys.argv = ["", "", "",]
    >>> _xmldoc_path = xmldoc_path()
    >>> sys.stdout = save_stdout
    >>> USAGE == temp_stdout.getvalue()[:-1]
    True

    Supply non-file argument.

    >>> save_stdout = sys.stdout
    >>> temp_stdout = StringIO()
    >>> sys.stdout = temp_stdout
    >>> _xmldoc_path = os.path.join(
    ...                    os.path.dirname(
    ...                        os.path.abspath(__file__)),
    ...                    TEST_PATH)
    >>> sys.argv = ["", _xmldoc_path]
    >>> _xmldoc_path = xmldoc_path()
    >>> sys.stdout = save_stdout
    >>> USAGE == temp_stdout.getvalue()[:-1]
    True

    Supply nonexistent file argument.

    >>> save_stdout = sys.stdout
    >>> temp_stdout = StringIO()
    >>> sys.stdout = temp_stdout
    >>> _xmldoc_path = os.path.join(
    ...                    os.path.dirname(
    ...                        os.path.abspath(__file__)),
    ...                    TEST_PATH, "xxxxx")
    >>> sys.argv = ["", _xmldoc_path]
    >>> _xmldoc_path = xmldoc_path()
    >>> sys.stdout = save_stdout
    >>> USAGE == temp_stdout.getvalue()[:-1]
    True

    Supply valid XML document path argument.

    >>> _xmldoc_path = os.path.join(
    ...                    os.path.dirname(
    ...                        os.path.abspath(__file__)),
    ...                    TEST_PATH, "xml","*","*.xml")
    >>> _xmldoc_path = glob.glob(_xmldoc_path)[0]
    >>> sys.argv = ["", _xmldoc_path]
    >>> _xmldoc_path == xmldoc_path()
    True
    """

    path = None
    try:
        if len(sys.argv) == 2:
            if sys.argv[1] == "-t" or sys.argv[1] == "--test":
                _test()
            else:
                path = sys.argv[1]
                if not os.path.exists(path):
                    raise IOError(path + \
                                  " does not exist.")
                elif not os.path.isfile(path):
                    raise IOError(path + \
                                  " is not a file.")
        else:
            raise IOError("Incorrect number of arguments supplied.")
    except IOError:
        print USAGE
    return path


def xmldoc(path):
    """
    Return the XML document as a list of strings from a file at path.

    Get the test reference data.

    >>> xmlref = os.path.join(
    ...              os.path.dirname(
    ...                  os.path.abspath(__file__)),
    ...               TEST_PATH, "xmlref.py")
    >>> namespace = {}
    >>> execfile(xmlref, globals(), namespace)
    >>> xml_doc_lens = namespace["XML_DOC_LENS"]
    >>> xml_doc_md5s = namespace["XML_DOC_MD5S"]

    Pick a test document.

    >>> xmldoc_glob = os.path.join(
    ...                   os.path.dirname(
    ...                       os.path.abspath(__file__)),
    ...                   TEST_PATH, "xml","*","*.xml")
    >>> _xmldoc_path = glob.glob(xmldoc_glob)[0]
    >>> _xmldoc = xmldoc(_xmldoc_path)

    Verify the test document matches the reference data.

    >>> _xmldoc[0] == '<?xml version="1.0" encoding="utf-8"?>\\n'
    True
    >>> _xmldoc[-1] == '</root>\\n'
    True
    >>> len(_xmldoc) == xml_doc_lens[os.path.basename(_xmldoc_path)]
    True
    >>> doc_hash = hashlib.md5()
    >>> doc_hash.update("".join(_xmldoc))
    >>> doc_hash.hexdigest() == xml_doc_md5s[os.path.basename(_xmldoc_path)]
    True
    """

    _xmldoc = None
    with open(path) as handle:
        _xmldoc = handle.readlines()

    return _xmldoc


def _main():
    """
    Run module as script.

    Test silent import.

    >>> from parse import _main
    """

    _xmldoc_path = xmldoc_path()
    if _xmldoc_path:
        _xmldoc = xmldoc(_xmldoc_path)
        print len(_xmldoc)

    return

if __name__ == "__main__":
    _main()