def bioodo_aggregation_fixture(request, tmpdir_factory):
# NB: fmtdict is a dictionary, potentially pointing to
# multiple output files; if so the multiple files must be put
# in the same directory
module, command, version, end, fmtdict = request.param
params = {'version': version, 'end': end}
keys = kwargs.get("keys", fmtdict.keys())
outputs = [fmtdict[k].format(**params)
for k in keys] * len(range(repeat))
# Add applications/module prefix
sources = [os.path.join("applications", module, output)
for output in outputs]
# Extract source basenames
dests = [os.path.basename(src) for src in outputs]
# Generate a unique test output directory
fdir = os.path.join(module, str(version), command, end)
# Make a temporary directory using unique test directory name
pdir = factories.safe_mktemp(tmpdir_factory, fdir)
# Symlink pytest_ngsfixtures files to temporary directory; the
# safe_symlink function automagically uses pytest_ngsfixtures
# installation directory to infer location of src
count = 0
for src, dst in zip(sources, dests):
rdir = pdir.mkdir(str(count))
factories.safe_symlink(rdir, src, dst)
count += 1
return module, command, version, end, pdir
def data(request, tmpdir_factory):
"""Generate fixture for rule"""
app, rule = request.param
if request.function.__name__ == "test_run":
d = ruleinfo.parse_rule(rule)
d['app'] = app
logger.info("Setting up fixture for {}".format(d['name']))
fixture_dir = os.path.join(app, d['name'])
fixture = factories.safe_mktemp(tmpdir_factory, fixture_dir)
inputmap = set_inputmap(d)
wildcards = utils.get_wildcards(inputmap, d['wildcard_constraints'])
try:
output = set_output(d, wildcards)
except:
output = None
for wc, src in inputmap:
if src:
if isinstance(src, str):
p = factories.safe_symlink(fixture, src, basename(src))
else:
for s in src:
p = factories.safe_symlink(fixture, s, basename(s))
else:
output = None
fixture_dir = os.path.join(app, os.path.splitext(basename(rule))[0])
fixture = factories.safe_mktemp(tmpdir_factory, fixture_dir)
if request.config.option.ngs_show_fixture:
logger.info("fixture directory: {}".format(str(fixture)))
return app, rule, output, fixture
def test_safe_symlink(tmpdir_factory, bam):
p = tmpdir_factory.mktemp("safe_symlink")
# Test using string as input without capturing return
safe_symlink(p, bamfile, "bar/foo.bar")
assert str(p).endswith("safe_symlink0")
# Test using string as input
l = safe_symlink(p, bamfile, "foo/foo.bar")
assert str(l).endswith("foo/foo.bar")
assert l.realpath() == bamfile_realpath
# Test using localpath as input
l = safe_symlink(p, bam, "foo.bar")
assert l.realpath() == bam.realpath()
assert str(l).endswith("foo.bar")
def ao(request, tmpdir_factory):
app, command, version, end, fmtdict = request.param
params = {'version': version, 'end': end}
outputs = [fmt.format(**params) for fmt in fmtdict.values()]
sources = [os.path.join("applications", app, output) for output in outputs]
dests = [os.path.basename(src) for src in sources]
fdir = os.path.join(app, str(version), command, end)
pdir = safe_mktemp(tmpdir_factory, fdir)
for src, dst in zip(sources, dests):
p = safe_symlink(pdir, src, dst)
return pdir
def bioodo_fixture(request, tmpdir_factory):
# NB: fmtdict is a dictionary, potentially pointing to
# multiple output files
module, command, version, end, fmtdict = request.param
params = {'version': version, 'end': end}
# Generate pytest_ngsfixtures application output names relative to
# applications/module directory
outputs = [fmt.format(**params) for fmt in fmtdict.values()]
# Add applications/module prefix
sources = [os.path.join("applications", module, output)
for output in outputs]
# Extract source basenames
dests = [os.path.basename(src) for src in sources]
# Generate a unique test output directory name
fdir = os.path.join(module, str(version), command, end)
# Make a temporary directory using unique test directory name
pdir = factories.safe_mktemp(tmpdir_factory, fdir)
# Symlink pytest_ngsfixtures files to temporary directory; the
# safe_symlink function automagically uses pytest_ngsfixtures
# installation directory to infer location of src
for src, dst in zip(sources, dests):
factories.safe_symlink(pdir, src, dst)
return module, command, version, end, pdir