--- a/env/lib/python3.7/site-packages/galaxy/util/properties.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,238 +0,0 @@
-""" Module used to blend ini, environment, and explicit dictionary properties
-to determine application configuration. Some hard coded defaults for Galaxy but
-this should be reusable by tool shed and pulsar as well.
-"""
-import os
-import os.path
-import sys
-from functools import partial
-from itertools import product, starmap
-
-import yaml
-from six import iteritems, string_types
-from six.moves.configparser import ConfigParser
-
-from galaxy.exceptions import InvalidFileFormatError
-from galaxy.util.path import extensions, has_ext, joinext
-
-
-def find_config_file(names, exts=None, dirs=None, include_samples=False):
-    """Locate a config file in multiple directories, with multiple extensions.
-
-    >>> from shutil import rmtree
-    >>> from tempfile import mkdtemp
-    >>> def touch(d, f):
-    ...     open(os.path.join(d, f), 'w').close()
-    >>> def _find_config_file(*args, **kwargs):
-    ...     return find_config_file(*args, **kwargs).replace(d, '')
-    >>> d = mkdtemp()
-    >>> d1 = os.path.join(d, 'd1')
-    >>> d2 = os.path.join(d, 'd2')
-    >>> os.makedirs(d1)
-    >>> os.makedirs(d2)
-    >>> touch(d1, 'foo.ini')
-    >>> touch(d1, 'foo.bar')
-    >>> touch(d1, 'baz.ini.sample')
-    >>> touch(d2, 'foo.yaml')
-    >>> touch(d2, 'baz.yml')
-    >>> _find_config_file('foo', dirs=(d1, d2))
-    '/d1/foo.ini'
-    >>> _find_config_file('baz', dirs=(d1, d2))
-    '/d2/baz.yml'
-    >>> _find_config_file('baz', dirs=(d1, d2), include_samples=True)
-    '/d2/baz.yml'
-    >>> _find_config_file('baz', dirs=(d1,), include_samples=True)
-    '/d1/baz.ini.sample'
-    >>> _find_config_file('foo', dirs=(d2, d1))
-    '/d2/foo.yaml'
-    >>> find_config_file('quux', dirs=(d,))
-    >>> _find_config_file('foo', exts=('bar', 'ini'), dirs=(d1,))
-    '/d1/foo.bar'
-    >>> rmtree(d)
-    """
-    found = __find_config_files(
-        names,
-        exts=exts or extensions['yaml'] + extensions['ini'],
-        dirs=dirs or [os.getcwd(), os.path.join(os.getcwd(), 'config')],
-        include_samples=include_samples,
-    )
-    if not found:
-        return None
-    # doesn't really make sense to log here but we should probably generate a warning of some kind if more than one
-    # config is found.
-    return found[0]
-
-
-def load_app_properties(
-    kwds=None,
-    ini_file=None,
-    ini_section=None,
-    config_file=None,
-    config_section=None,
-    config_prefix="GALAXY_CONFIG_"
-):
-    if config_file is None:
-        config_file = ini_file
-        config_section = ini_section
-
-    # read from file or init w/no file
-    if config_file:
-        properties = read_properties_from_file(config_file, config_section)
-    else:
-        properties = {'__file__': None}
-
-    # update from kwds
-    if kwds:
-        properties.update(kwds)
-
-    # update from env
-    override_prefix = "%sOVERRIDE_" % config_prefix
-    for key in os.environ:
-        if key.startswith(override_prefix):
-            config_key = key[len(override_prefix):].lower()
-            properties[config_key] = os.environ[key]
-        elif key.startswith(config_prefix):
-            config_key = key[len(config_prefix):].lower()
-            if config_key not in properties:
-                properties[config_key] = os.environ[key]
-
-    return properties
-
-
-def read_properties_from_file(config_file, config_section=None):
-    properties = {}
-    if has_ext(config_file, 'yaml', aliases=True, ignore='sample'):
-        if config_section is None:
-            config_section = "galaxy"
-        properties.update(__default_properties(config_file))
-        raw_properties = _read_from_yaml_file(config_file)
-        if raw_properties:
-            properties.update(raw_properties.get(config_section) or {})
-    elif has_ext(config_file, 'ini', aliases=True, ignore='sample'):
-        if config_section is None:
-            config_section = "app:main"
-        parser = nice_config_parser(config_file)  # default properties loaded w/parser
-        if parser.has_section(config_section):
-            properties.update(dict(parser.items(config_section)))
-        else:
-            properties.update(parser.defaults())
-    else:
-        raise InvalidFileFormatError()
-    return properties
-
-
-def _read_from_yaml_file(path):
-    with open(path, "r") as f:
-        return yaml.safe_load(f)
-
-
-def nice_config_parser(path):
-    parser = NicerConfigParser(path, defaults=__default_properties(path))
-    parser.optionxform = str  # Don't lower-case keys
-    with open(path) as f:
-        parser.read_file(f)
-    return parser
-
-
-class NicerConfigParser(ConfigParser):
-
-    def __init__(self, filename, *args, **kw):
-        ConfigParser.__init__(self, *args, **kw)
-        self.filename = filename
-        if hasattr(self, '_interpolation'):
-            self._interpolation = self.InterpolateWrapper(self._interpolation)
-
-    read_file = getattr(ConfigParser, 'read_file', ConfigParser.readfp)
-
-    def defaults(self):
-        """Return the defaults, with their values interpolated (with the
-        defaults dict itself)
-
-        Mainly to support defaults using values such as %(here)s
-        """
-        defaults = ConfigParser.defaults(self).copy()
-        for key, val in iteritems(defaults):
-            defaults[key] = self.get('DEFAULT', key) or val
-        return defaults
-
-    def _interpolate(self, section, option, rawval, vars):
-        # Python < 3.2
-        try:
-            return ConfigParser._interpolate(
-                self, section, option, rawval, vars)
-        except Exception:
-            e = sys.exc_info()[1]
-            args = list(e.args)
-            args[0] = 'Error in file %s: %s' % (self.filename, e)
-            e.args = tuple(args)
-            e.message = args[0]
-            raise
-
-    class InterpolateWrapper(object):
-        # Python >= 3.2
-        def __init__(self, original):
-            self._original = original
-
-        def __getattr__(self, name):
-            return getattr(self._original, name)
-
-        def before_get(self, parser, section, option, value, defaults):
-            try:
-                return self._original.before_get(parser, section, option,
-                                                 value, defaults)
-            except Exception:
-                e = sys.exc_info()[1]
-                args = list(e.args)
-                args[0] = 'Error in file %s: %s' % (parser.filename, e)
-                e.args = tuple(args)
-                e.message = args[0]
-                raise
-
-
-def _running_from_source():
-    paths = ['run.sh', 'lib/galaxy/__init__.py', 'scripts/common_startup.sh']
-    return all(map(os.path.exists, paths))
-
-
-running_from_source = _running_from_source()
-
-
-def get_data_dir(properties):
-    data_dir = properties.get('data_dir', None)
-    if data_dir is None:
-        if running_from_source:
-            data_dir = './database'
-        else:
-            config_dir = properties.get('config_dir', os.path.dirname(properties['__file__']))
-            data_dir = os.path.join(config_dir, 'data')
-    return data_dir
-
-
-def __get_all_configs(dirs, names):
-    return list(filter(os.path.exists, starmap(os.path.join, product(dirs, names))))
-
-
-def __find_config_files(names, exts=None, dirs=None, include_samples=False):
-    sample_names = []
-    if isinstance(names, string_types):
-        names = [names]
-    if not dirs:
-        dirs = [os.getcwd()]
-    if exts:
-        # add exts to names, converts back into a list because it's going to be small and we might consume names twice
-        names = list(starmap(joinext, product(names, exts)))
-    if include_samples:
-        sample_names = map(partial(joinext, ext='sample'), names)
-    # check for all names in each dir before moving to the next dir. could do it the other way around but that makes
-    # less sense to me.
-    return __get_all_configs(dirs, names) or __get_all_configs(dirs, sample_names)
-
-
-def __default_properties(path):
-    return {
-        'here': os.path.dirname(os.path.abspath(path)),
-        '__file__': os.path.abspath(path)
-    }
-
-
-__all__ = ('find_config_file', 'get_data_dir', 'load_app_properties', 'NicerConfigParser', 'running_from_source')