def test_plugin_cleanup():
for p in init_plugins():
deactivate(p)
# cleanup after testing pluging
genome_dir = os.path.join(os.getcwd(), ".genomepy_plugin_tests")
genomepy.utils.rm_rf(genome_dir)
def manage_plugins(command, plugin_names=None):
"""Enable or disable plugins.
"""
if plugin_names is None:
plugin_names = []
active_plugins = config.get("plugin", [])
plugins = init_plugins()
if command == "enable":
for name in plugin_names:
if name not in plugins:
raise ValueError("Unknown plugin: {}".format(name))
if name not in active_plugins:
active_plugins.append(name)
elif command == "disable":
for name in plugin_names:
if name in active_plugins:
active_plugins.remove(name)
elif command == "list":
print("{:20}{}".format("plugin", "enabled"))
for plugin in sorted(plugins):
print("{:20}{}".format(plugin, {
False: "",
True: "*"
}[plugin in active_plugins]))
else:
raise ValueError("Invalid plugin command")
config["plugin"] = active_plugins
config.save()
if command in ["enable", "disable"]:
print("Enabled plugins: {}".format(", ".join(sorted(active_plugins))))
def genome(request, tempdir):
"""Create a test genome."""
name = "dm3" # Use fake name for blacklist test
fafile = "tests/data/small_genome.fa"
# Input needs to be bgzipped, depending on param
if os.path.exists(fafile + ".gz"):
if request.param == "unzipped":
check_call(["gunzip", fafile + ".gz"])
elif request.param == "bgzipped":
check_call(["bgzip", fafile])
tmpdir = os.path.join(tempdir, request.param, name)
os.makedirs(tmpdir)
if request.param == "bgzipped":
fafile += ".gz"
copyfile(fafile, os.path.join(tmpdir, os.path.basename(fafile)))
for p in init_plugins():
activate(p)
# provide the fixture value
yield Genome(name, genome_dir=os.path.join(tempdir, request.param))
if os.path.exists(fafile) and request.param == "unzipped":
check_call(["bgzip", fafile])
def manage_plugins(command, plugin_names=None):
"""List, enable or disable plugins."""
plugins = init_plugins()
for name in plugin_names if plugin_names else []:
if name not in plugins:
raise ValueError(f"Unknown plugin: {name}")
active_plugins = config.get("plugin", [])
if command == "list":
print("{:20}{}".format("plugin", "enabled"))
for plugin in sorted(plugins):
print("{:20}{}".format(plugin, {
False: "",
True: "*"
}[plugin in active_plugins]))
return
elif command in ["enable", "activate"]:
for name in plugin_names:
if name not in active_plugins:
active_plugins.append(name)
elif command in ["disable", "deactivate"]:
for name in plugin_names:
if name in active_plugins:
active_plugins.remove(name)
else:
raise ValueError(f"Invalid plugin command: {command}")
config["plugin"] = active_plugins
config.save()
print("Enabled plugins: {}".format(", ".join(sorted(active_plugins))))
def manage_plugins(command, plugin_names=None):
"""Enable or disable plugins.
"""
if plugin_names is None:
plugin_names = []
active_plugins = config.get("plugin", [])
plugins = init_plugins()
if command == "enable":
for name in plugin_names:
if name not in plugins:
raise ValueError("Unknown plugin: {}".format(name))
if name not in active_plugins:
active_plugins.append(name)
elif command == "disable":
for name in plugin_names:
if name in active_plugins:
active_plugins.remove(name)
elif command == "list":
print("{:20}{}".format("plugin", "enabled"))
for plugin in sorted(plugins):
print("{:20}{}".format(plugin, {False:"", True:"*"}[plugin in active_plugins]))
else:
raise ValueError("Invalid plugin command")
config["plugins"] = active_plugins
config.save()
if command in ["enable", "disable"]:
print("Enabled plugins: {}".format(", ".join(sorted(active_plugins))))
def test_plugins():
# activate and check all plugins
for p in init_plugins():
if p not in ["blacklist", "star"]:
assert genomepy.utils.cmd_ok(p)
elif p == "star":
assert genomepy.utils.cmd_ok(p.upper())
activate(p)
def genome(tempdir):
"""Create a test genome."""
name = "small_genome"
fafile = "tests/data/small_genome.fa"
if os.path.exists(fafile + ".gz"):
check_call(["gunzip", fafile + ".gz"])
os.mkdir(os.path.join(tempdir, name))
copyfile(fafile, os.path.join(tempdir, name, os.path.basename(fafile)))
for p in init_plugins():
activate(p)
yield Genome(name, genome_dir=tempdir) # provide the fixture value
if os.path.exists(fafile):
check_call(["gzip", fafile])