root/spongenet/trunk/spongenet/query.py

#!/usr/bin/env python

"""
Create CSV spreadsheets from sponge data NetCDF files.

Usage:

   > python query.py path/to/config/file
   > python query.py -t
   > python query.py --test

Test silent import:

>>> import expand
"""

__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 zipfile
import shutil
import fileinput
import doctest
import unittest
from StringIO import StringIO

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


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

    Test silent import:

    >>> from expand import _test
    """

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

    return


def config_path():
    """
    Return the configuration 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 = []
    >>> _config_path = config_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 = ["", "", "",]
    >>> _config_path = config_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
    >>> _config_path = os.path.join(
    ...                    os.path.dirname(
    ...                        os.path.abspath(__file__)),
    ...                    TEST_PATH)
    >>> sys.argv = ["", _config_path]
    >>> _config_path = config_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
    >>> _config_path = os.path.join(
    ...                    os.path.dirname(
    ...                        os.path.abspath(__file__)),
    ...                    TEST_PATH, "xxxxx")
    >>> sys.argv = ["", _config_path]
    >>> _config_path = config_path()
    >>> sys.stdout = save_stdout
    >>> USAGE == temp_stdout.getvalue()[:-1]
    True

    Supply valid config path argument:

    >>> _config_path = os.path.join(
    ...                    os.path.dirname(
    ...                        os.path.abspath(__file__)),
    ...                    TEST_PATH, "config.py")
    >>> sys.argv = ["", _config_path]
    >>> _config_path == config_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 config(path):
    """
    Return the configuration from a file.

    Execute empty configuration:

    >>> _config_path = os.path.join(
    ...                    os.path.dirname(
    ...                        os.path.abspath(__file__)),
    ...                    TEST_PATH, "empty_config.py")
    >>> ncdir,csvdir, \
            ncfile_pattern,csvfile_pattern, \
            location,platform,packages = \
            config(_config_path)
    >>> ncdir
    >>> csvdir
    >>> ncfile_pattern
    >>> csvfile_pattern
    >>> location
    >>> platform
    >>> packages

    Execute nonexistent configuration:

    >>> save_stdout = sys.stdout
    >>> temp_stdout = StringIO()
    >>> sys.stdout = temp_stdout
    >>> _config_path = os.path.join(
    ...                    os.path.dirname(
    ...                        os.path.abspath(__file__)),
    ...                    TEST_PATH, "xxxxx")
    >>> ncdir,csvdir, \
            ncfile_pattern,csvfile_pattern, \
            location,platform,packages = \
            config(_config_path)
    >>> sys.stdout = save_stdout
    >>> USAGE == temp_stdout.getvalue()[:-1]
    True
    >>> ncdir
    >>> csvdir
    >>> ncfile_pattern
    >>> csvfile_pattern
    >>> location
    >>> platform
    >>> packages

    Execute bad configuration:

    >>> save_stdout = sys.stdout
    >>> temp_stdout = StringIO()
    >>> sys.stdout = temp_stdout
    >>> _config_path = os.path.join(
    ...                    os.path.dirname(
    ...                        os.path.abspath(__file__)),
    ...                    TEST_PATH, "bad_config.py")
    >>> ncdir,csvdir, \
            ncfile_pattern,csvfile_pattern, \
            location,platform,packages = \
            config(_config_path)
    >>> sys.stdout = save_stdout
    >>> USAGE == temp_stdout.getvalue()[:-1]
    True
    >>> ncdir
    >>> csvdir
    >>> ncfile_pattern
    >>> csvfile_pattern
    >>> location
    >>> platform
    >>> packages

    Execute valid configuration:

    >>> _config_path = os.path.join(
    ...                    os.path.dirname(
    ...                        os.path.abspath(__file__)),
    ...                    TEST_PATH, "config.py")
    >>> ncdir,csvdir, \
            ncfile_pattern,csvfile_pattern, \
            location,platform,packages = \
            config(_config_path)
    >>> ncdir == os.path.join(os.path.dirname(os.path.abspath(__file__)),
    ...                       TEST_PATH, "nc")
    True
    >>> csvdir == os.path.join(os.path.dirname(os.path.abspath(__file__)),
    ...                        TEST_PATH, "csv")
    True
    >>> ncfile_pattern == "%(location)s_%(platform)s_%(package)s_" \
                          "[0-9][0-9][0-9][0-9]_[0-9][0-9].nc"
    True
    >>> csvfile_pattern == "%(location)s_%(platform)s_%(package)s_" \
                           "[0-9][0-9][0-9][0-9]_[0-9][0-9].csv"
    True
    >>> location == "location"
    True
    >>> platform == "platform"
    True
    >>> packages == ('system',
    ...              'turbidity',
    ...              'optode_127',
    ...              'optode_167',
    ...              'optode_169',
    ...              'optode_170',
    ...              'optode_171',
    ...              'optode_172',
    ...              'optode_173',
    ...              'optode_175',
    ...              'optode_176',
    ...              'optode_178',
    ...              'optode_179',
    ...              'conductivity',
    ...              'pressure',
    ...              'current',
    ...             )
    True
    """

    namespace = {}
    namespace["NCDIR"] = None
    namespace["CSVDIR"] = None
    namespace["NCFILE_PATTERN"] = None
    namespace["CSVFILE_PATTERN"] = None
    namespace["LOCATION"] = None
    namespace["PLATFORM"] = None
    namespace["PACKAGES"] = None
    try:
        execfile(path, globals(), namespace)
    except IOError:
        print USAGE
    except SyntaxError:
        print USAGE
    return (namespace["NCDIR"],
            namespace["CSVDIR"],
            namespace["NCFILE_PATTERN"],
            namespace["CSVFILE_PATTERN"],
            namespace["LOCATION"],
            namespace["PLATFORM"],
            namespace["PACKAGES"],
           )


def query(ncdir, csvdir,
          ncfile_pattern, csvfile_pattern,
          location, platform, packages):
    """
    Create CSV spreadsheets from sponge data NetCDF files.
    """

    return


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

    Supply incomplete config file:

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

    _config_path = config_path()
    if _config_path:
        _config = config(_config_path)
        if all(_config):
            query(*_config)
        else:
            print USAGE
    return

if __name__ == "__main__":
    _main()