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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Path mapping for various test resources.
"""
import os
import sys
import tempfile
from dendropy.utility import messaging
from dendropy.utility.timeprocessing import pretty_timestamp
_LOG = messaging.get_logger(__name__)
try:
import pkg_resources
# TESTS_DIR = pkg_resources.resource_filename("dendropy", os.path.join(os.pardir, "tests"))
TESTS_DIR = pkg_resources.resource_filename("dendropy", "test")
APPLICATIONS_DIR = pkg_resources.resource_filename("dendropy", os.path.join(os.pardir, "applications"))
_LOG.info("using pkg_resources path mapping")
except:
LOCAL_DIR = os.path.dirname(__file__)
TESTS_DIR = os.path.join(LOCAL_DIR, os.path.pardir)
PACKAGE_DIR = os.path.join(TESTS_DIR, os.path.pardir)
APPLICATIONS_DIR = os.path.join(PACKAGE_DIR, os.path.pardir, "applications")
_LOG.info("using local filesystem path mapping")
TESTS_DATA_DIR = os.path.join(TESTS_DIR, "data")
TESTS_OUTPUT_DIR = os.path.join(TESTS_DIR, "output")
TESTS_COVERAGE_DIR = os.path.join(TESTS_DIR, "coverage")
TESTS_COVERAGE_REPORT_DIR = os.path.join(TESTS_COVERAGE_DIR, "report")
TESTS_COVERAGE_SOURCE_DIR = os.path.join(TESTS_COVERAGE_DIR, "source")
def tree_source_stream(filename):
if not (sys.version_info.major >= 3 and sys.version_info.minor >= 4):
return open(tree_source_path(filename), "rU")
else:
return open(tree_source_path(filename), "r")
def tree_source_path(filename=None):
if filename is None:
filename = ""
return os.path.join(TESTS_DATA_DIR, "trees", filename)
def char_source_stream(filename):
return open(char_source_path(filename), "rU")
def char_source_path(filename=None):
if filename is None:
filename = ""
return os.path.join(TESTS_DATA_DIR, "chars", filename)
def mixed_source_stream(filename):
return open(mixed_source_path(filename), "rU")
def mixed_source_path(filename=None):
if filename is None:
filename = ""
return os.path.join(TESTS_DATA_DIR, "mixed", filename)
def splits_source_stream(filename):
if not (sys.version_info.major >= 3 and sys.version_info.minor >= 4):
return open(splits_source_path(filename), "rU")
else:
return open(splits_source_path(filename), "r")
def splits_source_path(filename=None):
if filename is None:
filename = ""
return os.path.join(TESTS_DATA_DIR, "splits", filename)
def other_source_stream(filename):
if not (sys.version_info.major >= 3 and sys.version_info.minor >= 4):
return open(other_source_path(filename), "rU")
else:
return open(other_source_path(filename), "r")
def other_source_path(filename=None):
if filename is None:
filename = ""
return os.path.join(TESTS_DATA_DIR, "other", filename)
def data_source_stream(filename):
return open(data_source_path(filename), "rU")
def data_source_path(filename=None):
if filename is None:
filename = ""
elif isinstance(filename, list):
filename = os.path.sep.join(filename)
return os.path.join(TESTS_DATA_DIR, filename)
def named_output_stream(filename=None, suffix_timestamp=True):
return open(named_output_path(filename=filename, suffix_timestamp=suffix_timestamp), "w")
def named_output_path(filename=None, suffix_timestamp=True):
if filename is None:
filename = ""
else:
if isinstance(filename, list):
filename = os.path.sep.join(filename)
if suffix_timestamp:
filename = "%s.%s" % (filename, pretty_timestamp(style=1))
if not os.path.exists(TESTS_OUTPUT_DIR):
os.makedirs(TESTS_OUTPUT_DIR)
return os.path.join(TESTS_OUTPUT_DIR, filename)
def application_source_path(filename=None):
if filename is None:
filename = ""
return os.path.join(APPLICATIONS_DIR, filename)
class SandboxedFile(object):
def __init__(self, mode="w"):
self.mode = mode
self.fileobj = None
self.filepath = None
def __enter__(self):
self.fileobj = tempfile.NamedTemporaryFile(
mode=self.mode,
delete=False)
self.filepath = self.fileobj.name
return self.fileobj
def __exit__(self, exc_type, exc_value, traceback):
try:
self.fileobj.flush()
self.fileobj.close()
except ValueError:
# If client code closes:
# ValueError: I/O operation on closed file.
pass
try:
os.remove(self.filepath)
except OSError:
pass
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