def test_copy_file__overwrite(temp_folder):
with SetWorkingDirectory(temp_folder):
set_file_contents("file_1", "4")
set_file_contents("file_2", "5")
copy_file("file_1", "file_2")
assert_equal(set(os.listdir(".")), set(["file_1", "file_2"]))
assert_equal(get_file_contents("file_1"), "4")
assert_equal(get_file_contents("file_2"), "4")
def _teardown(self, config, temp):
fileutils.make_dirs(self._root)
fileutils.move_file(os.path.join(temp, "summary.html"),
os.path.join(self._root, "summary.html"))
css_path = paleomix.resources.report("zonkey", "report.css")
fileutils.copy_file(css_path, os.path.join(self._root, "summary.css"))
def test_copy_file__overwrite(temp_folder):
with SetWorkingDirectory(temp_folder):
set_file_contents("file_1", "4")
set_file_contents("file_2", "5")
copy_file("file_1", "file_2")
assert_equal(set(os.listdir(".")), set(["file_1", "file_2"]))
assert_equal(get_file_contents("file_1"), "4")
assert_equal(get_file_contents("file_2"), "4")
def test_copy_file__copy_to_different_folder(temp_folder):
with SetWorkingDirectory(temp_folder):
set_file_contents("file_1", "3")
copy_file("file_1", "dst/file_1")
assert_equal(set(os.listdir(".")), set(["file_1", "dst"]))
assert_equal(os.listdir("dst"), ["file_1"])
assert_equal(get_file_contents("file_1"), "3")
assert_equal(get_file_contents("dst/file_1"), "3")
def _teardown(self, config, temp):
fileutils.make_dirs(self._root)
fileutils.move_file(os.path.join(temp, "report.html"),
os.path.join(self._root, "report.html"))
css_path = paleomix.resources.report("zonkey", "report.css")
fileutils.copy_file(css_path, os.path.join(self._root, "report.css"))
def test_copy_file__copy_to_different_folder(temp_folder):
with SetWorkingDirectory(temp_folder):
set_file_contents("file_1", "3")
copy_file("file_1", "dst/file_1")
assert_equal(set(os.listdir(".")), set(["file_1", "dst"]))
assert_equal(os.listdir("dst"), ["file_1"])
assert_equal(get_file_contents("file_1"), "3")
assert_equal(get_file_contents("dst/file_1"), "3")
def test_copy_file__simple_copy_in_cwd(temp_folder):
with SetWorkingDirectory(temp_folder):
assert_equal(os.listdir("."), [])
set_file_contents("file_1", "1")
assert_equal(os.listdir("."), ["file_1"])
copy_file("file_1", "file_2")
assert_equal(set(os.listdir(".")), set(["file_1", "file_2"]))
assert_equal(get_file_contents("file_1"), "1")
assert_equal(get_file_contents("file_2"), "1")
def test_copy_file__simple_copy_in_cwd(temp_folder):
with SetWorkingDirectory(temp_folder):
assert_equal(os.listdir("."), [])
set_file_contents("file_1", "1")
assert_equal(os.listdir("."), ["file_1"])
copy_file("file_1", "file_2")
assert_equal(set(os.listdir(".")), set(["file_1", "file_2"]))
assert_equal(get_file_contents("file_1"), "1")
assert_equal(get_file_contents("file_2"), "1")
def test_copy_file__copy_to_new_folder(temp_folder):
assert make_dirs(os.path.join(temp_folder, "src"))
file_1 = os.path.join(temp_folder, "src", "file_1")
file_2 = os.path.join(temp_folder, "dst", "file_2")
set_file_contents(file_1, "2")
copy_file(file_1, file_2)
assert_equal(os.listdir(os.path.dirname(file_1)), ["file_1"])
assert_equal(os.listdir(os.path.dirname(file_2)), ["file_2"])
assert_equal(get_file_contents(file_1), "2")
assert_equal(get_file_contents(file_2), "2")
def test_copy_file__simple_copy(temp_folder):
file_1 = os.path.join(temp_folder, "file_1")
file_2 = os.path.join(temp_folder, "file_2")
assert_equal(os.listdir(temp_folder), [])
set_file_contents(file_1, "1")
assert_equal(os.listdir(temp_folder), ["file_1"])
copy_file(file_1, file_2)
assert_equal(set(os.listdir(temp_folder)), set(["file_1", "file_2"]))
assert_equal(get_file_contents(file_1), "1")
assert_equal(get_file_contents(file_2), "1")
def test_copy_file__copy_to_new_folder(temp_folder):
assert make_dirs(os.path.join(temp_folder, "src"))
file_1 = os.path.join(temp_folder, "src", "file_1")
file_2 = os.path.join(temp_folder, "dst", "file_2")
set_file_contents(file_1, "2")
copy_file(file_1, file_2)
assert_equal(os.listdir(os.path.dirname(file_1)), ["file_1"])
assert_equal(os.listdir(os.path.dirname(file_2)), ["file_2"])
assert_equal(get_file_contents(file_1), "2")
assert_equal(get_file_contents(file_2), "2")
def test_copy_file__simple_copy(temp_folder):
file_1 = os.path.join(temp_folder, "file_1")
file_2 = os.path.join(temp_folder, "file_2")
assert_equal(os.listdir(temp_folder), [])
set_file_contents(file_1, "1")
assert_equal(os.listdir(temp_folder), ["file_1"])
copy_file(file_1, file_2)
assert_equal(set(os.listdir(temp_folder)), set(["file_1", "file_2"]))
assert_equal(get_file_contents(file_1), "1")
assert_equal(get_file_contents(file_2), "1")
def _teardown(self, config, temp):
for postfix in ("ALIGNMENT", "PARTITION"):
filenames = [self._kwargs["TEMP_IN_" + postfix],
self._kwargs["TEMP_IN_" + postfix] + ".reduced",
self._kwargs["OUT_" + postfix]]
for (source, destination) in zip(filenames, filenames[1:]):
source = fileutils.reroot_path(temp, source)
destination = fileutils.reroot_path(temp, destination)
if not os.path.exists(destination):
fileutils.copy_file(source, destination)
os.remove(source)
CommandNode._teardown(self, config, temp)
def _run(self, config, temp):
likelihoods = []
for fileset in self._files:
for filename in fileset:
if filename.endswith(".log"):
likelihoods.append(
(self._read_admixture_log(filename), fileset))
break
else:
raise NodeError("No log-file found in list of admixture "
"output-files: %r" % (fileset, ))
_, fileset = max(likelihoods)
for src_filename in fileset:
dst_filename = fileutils.reroot_path(self._output_root,
src_filename)
fileutils.copy_file(src_filename, dst_filename)
def _run(self, config, temp):
likelihoods = []
for fileset in self._files:
for filename in fileset:
if filename.endswith(".log"):
likelihoods.append((self._read_admixture_log(filename),
fileset))
break
else:
raise NodeError("No log-file found in list of admixture "
"output-files: %r" % (fileset,))
_, fileset = max(likelihoods)
for src_filename in fileset:
dst_filename = fileutils.reroot_path(self._output_root,
src_filename)
fileutils.copy_file(src_filename, dst_filename)
def _run(self, _config, _temp):
for (src_file, dst_file) in self._files:
copy_file(src_file, dst_file)
def _run(self, _config, _temp):
for (src_file, dst_file) in self._files:
copy_file(src_file, dst_file)