def test_builder__set_kwargs__after_finalize():
expected = {"IN_PATH" : "/a/b/"}
builder = AtomicCmdBuilder("echo")
builder.set_kwargs(IN_PATH = "/a/b/")
builder.finalize()
assert_raises(AtomicCmdBuilderError, builder.set_kwargs, OUT_PATH = "/dst/file")
assert_equal(builder.kwargs, expected)
def test_builder__set_kwargs__after_finalize():
expected = {"IN_PATH": "/a/b/"}
builder = AtomicCmdBuilder("echo")
builder.set_kwargs(IN_PATH="/a/b/")
builder.finalize()
assert_raises(AtomicCmdBuilderError,
builder.set_kwargs,
OUT_PATH="/dst/file")
assert_equal(builder.kwargs, expected)
def test_builder__finalize__calls_atomiccmd():
was_called = []
class _AtomicCmdMock:
def __init__(self, *args, **kwargs):
assert_equal(args, (["echo", "-out", "%(OUT_FILE)s", "%(IN_FILE)s"],))
assert_equal(kwargs, {"IN_FILE" : "/in/file", "OUT_FILE" : "/out/file", "set_cwd" : True})
was_called.append(True)
with Monkeypatch("pypeline.atomiccmd.builder.AtomicCmd", _AtomicCmdMock):
builder = AtomicCmdBuilder("echo", set_cwd = True)
builder.add_option("-out", "%(OUT_FILE)s")
builder.add_value("%(IN_FILE)s")
builder.set_kwargs(OUT_FILE = "/out/file",
IN_FILE = "/in/file")
builder.finalize()
assert was_called
def test_builder__finalize__calls_atomiccmd():
was_called = []
class _AtomicCmdMock:
def __init__(self, *args, **kwargs):
assert_equal(args,
(["echo", "-out", "%(OUT_FILE)s", "%(IN_FILE)s"], ))
assert_equal(kwargs, {
"IN_FILE": "/in/file",
"OUT_FILE": "/out/file",
"set_cwd": True
})
was_called.append(True)
with Monkeypatch("pypeline.atomiccmd.builder.AtomicCmd", _AtomicCmdMock):
builder = AtomicCmdBuilder("echo", set_cwd=True)
builder.add_option("-out", "%(OUT_FILE)s")
builder.add_value("%(IN_FILE)s")
builder.set_kwargs(OUT_FILE="/out/file", IN_FILE="/in/file")
builder.finalize()
assert was_called
def __init__(self, d_bam, dependencies):
aux_r = os.path.join(os.path.dirname(gccorrect.__file__), 'model_gc.R')
dest = os.path.join(d_bam.bam_output,
'%s_GC_Model.txt' % (str(d_bam.bam_name)))
plot_dest = os.path.splitext(dest)[0] + '.pdf'
infiles = [''.join(n.output_files) for n in dependencies]
builder = AtomicCmdBuilder(("Rscript", "%(AUX_R)s"))
builder.add_value('%(OUT_FILEPATH)s')
builder.add_value('%(OUT_PLOT)s')
builder.add_multiple_values(infiles)
builder.set_kwargs(AUX_R=aux_r,
OUT_FILEPATH=dest,
OUT_PLOT=plot_dest,
CHECK_VERSION=Rscript_VERSION)
cmd = builder.finalize()
d_bam.opts['BamInfo']['--GCmodel'] = dest
description = "<CreateGCModel: '%s' -> '%s'" % (d_bam.bam_temp_local,
dest)
CommandNode.__init__(self,
description=description,
command=cmd,
dependencies=dependencies)
def test_builder__finalize__returns_singleton():
builder = AtomicCmdBuilder("echo")
assert builder.finalize() is builder.finalize()
def _do_test_builder__add_or_set_option__after_finalize(setter):
builder = AtomicCmdBuilder("find")
builder.finalize()
assert_raises(AtomicCmdBuilderError, setter, builder, "-size", "1")
def test_builder__finalize__returns_singleton():
builder = AtomicCmdBuilder("echo")
assert builder.finalize() is builder.finalize()
def _do_test_builder__add_or_set_option__after_finalize(setter):
builder = AtomicCmdBuilder("find")
builder.finalize()
assert_raises(AtomicCmdBuilderError, setter, builder, "-size", "1")
