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"""
Test the plugin framework in sourmash.plugins, which uses importlib.metadata
entrypoints.
"""
import sys
import pytest
import collections
import sourmash
from sourmash.logging import set_quiet
import sourmash_tst_utils as utils
from sourmash import plugins
from sourmash.signature import load_one_signature_from_json
from sourmash.index import LinearIndex
from sourmash.save_load import Base_SaveSignaturesToLocation, SaveSignaturesToLocation
_Dist = collections.namedtuple("_Dist", ["version"])
class FakeEntryPoint:
"""
A class that stores a name and an object to be returned on 'load()'.
Mocks the EntryPoint class used by importlib.metadata.
"""
module = "test_plugin_framework"
dist = _Dist("0.1")
group = "groupfoo"
def __init__(self, name, load_obj, *, error_on_import=None):
self.name = name
self.load_obj = load_obj
self.error_on_import = error_on_import
def load(self):
if self.error_on_import is not None:
raise self.error_on_import("as requested")
return self.load_obj
#
# Test basic features of the load_from plugin hook.
#
class Test_EntryPointBasics_LoadFrom:
def get_some_sigs(self, location, *args, **kwargs):
ss2 = utils.get_test_data("2.fa.sig")
ss47 = utils.get_test_data("47.fa.sig")
ss63 = utils.get_test_data("63.fa.sig")
sig2 = load_one_signature_from_json(ss2, ksize=31)
sig47 = load_one_signature_from_json(ss47, ksize=31)
sig63 = load_one_signature_from_json(ss63, ksize=31)
lidx = LinearIndex([sig2, sig47, sig63], location)
return lidx
get_some_sigs.priority = 1
def setup_method(self):
self.saved_plugins = plugins._plugin_load_from
plugins._plugin_load_from = [
FakeEntryPoint("test_load", self.get_some_sigs),
FakeEntryPoint(
"test_load", self.get_some_sigs, error_on_import=ModuleNotFoundError
),
]
def teardown_method(self):
plugins._plugin_load_from = self.saved_plugins
def test_load_1(self):
ps = list(plugins.get_load_from_functions())
assert len(ps) == 1
def test_load_2(self, runtmp):
fake_location = runtmp.output("passed-through location")
idx = sourmash.load_file_as_index(fake_location)
print(idx, idx.location)
assert len(idx) == 3
assert idx.location == fake_location
class Test_EntryPoint_LoadFrom_Priority:
def get_some_sigs(self, location, *args, **kwargs):
ss2 = utils.get_test_data("2.fa.sig")
ss47 = utils.get_test_data("47.fa.sig")
ss63 = utils.get_test_data("63.fa.sig")
sig2 = load_one_signature_from_json(ss2, ksize=31)
sig47 = load_one_signature_from_json(ss47, ksize=31)
sig63 = load_one_signature_from_json(ss63, ksize=31)
lidx = LinearIndex([sig2, sig47, sig63], location)
return lidx
get_some_sigs.priority = 5
def set_called_flag_1(self, location, *args, **kwargs):
# high priority 1, raise ValueError
print("setting flag 1")
self.was_called_flag_1 = True
raise ValueError
set_called_flag_1.priority = 1
def set_called_flag_2(self, location, *args, **kwargs):
# high priority 2, return None
print("setting flag 2")
self.was_called_flag_2 = True
return None
set_called_flag_2.priority = 2
def set_called_flag_3(self, location, *args, **kwargs):
# lower priority 10, should not be called
print("setting flag 3")
self.was_called_flag_3 = True
return None
set_called_flag_3.priority = 10
def setup_method(self):
self.saved_plugins = plugins._plugin_load_from
plugins._plugin_load_from = [
FakeEntryPoint("test_load", self.get_some_sigs),
FakeEntryPoint("test_load_2", self.set_called_flag_1),
FakeEntryPoint("test_load_3", self.set_called_flag_2),
FakeEntryPoint("test_load_4", self.set_called_flag_3),
]
self.was_called_flag_1 = False
self.was_called_flag_2 = False
self.was_called_flag_3 = False
def teardown_method(self):
plugins._plugin_load_from = self.saved_plugins
def test_load_1(self):
ps = list(plugins.get_load_from_functions())
assert len(ps) == 4
assert not self.was_called_flag_1
assert not self.was_called_flag_2
assert not self.was_called_flag_3
def test_load_2(self, runtmp):
fake_location = runtmp.output("passed-through location")
idx = sourmash.load_file_as_index(fake_location)
print(idx, idx.location)
assert len(idx) == 3
assert idx.location == fake_location
assert self.was_called_flag_1
assert self.was_called_flag_2
assert not self.was_called_flag_3
#
# Test basic features of the save_to plugin hook.
#
class FakeSaveClass(Base_SaveSignaturesToLocation):
"""
A fake save class that just records what was sent to it.
"""
priority = 50
def __init__(self, location):
super().__init__(location)
self.keep = []
@classmethod
def matches(cls, location):
if location:
return location.endswith(".this-is-a-test")
def add(self, ss):
super().add(ss)
self.keep.append(ss)
class FakeSaveClass_HighPriority(FakeSaveClass):
priority = 1
class Test_EntryPointBasics_SaveTo:
# test the basics
def setup_method(self):
self.saved_plugins = plugins._plugin_save_to
plugins._plugin_save_to = [
FakeEntryPoint("test_save", FakeSaveClass),
FakeEntryPoint(
"test_save", FakeSaveClass, error_on_import=ModuleNotFoundError
),
]
def teardown_method(self):
plugins._plugin_save_to = self.saved_plugins
def test_save_1(self):
ps = list(plugins.get_save_to_functions())
print(ps)
assert len(ps) == 1
def test_save_2(self, runtmp):
# load some signatures to save
ss2 = utils.get_test_data("2.fa.sig")
ss47 = utils.get_test_data("47.fa.sig")
ss63 = utils.get_test_data("63.fa.sig")
sig2 = load_one_signature_from_json(ss2, ksize=31)
sig47 = load_one_signature_from_json(ss47, ksize=31)
sig63 = load_one_signature_from_json(ss63, ksize=31)
# build a fake location that matches the FakeSaveClass
# extension
fake_location = runtmp.output("out.this-is-a-test")
# this should use the plugin architecture to return an object
# of type FakeSaveClass, with the three signatures in it.
x = SaveSignaturesToLocation(fake_location)
with x as save_sig:
save_sig.add(sig2)
save_sig.add(sig47)
save_sig.add(sig63)
print(len(x))
print(x.keep)
assert isinstance(x, FakeSaveClass)
assert x.keep == [sig2, sig47, sig63]
class Test_EntryPointPriority_SaveTo:
# test that priority is observed
def setup_method(self):
self.saved_plugins = plugins._plugin_save_to
plugins._plugin_save_to = [
FakeEntryPoint("test_save", FakeSaveClass),
FakeEntryPoint("test_save2", FakeSaveClass_HighPriority),
]
def teardown_method(self):
plugins._plugin_save_to = self.saved_plugins
def test_save_1(self):
ps = list(plugins.get_save_to_functions())
print(ps)
assert len(ps) == 2
def test_save_2(self, runtmp):
# load some signatures to save
ss2 = utils.get_test_data("2.fa.sig")
ss47 = utils.get_test_data("47.fa.sig")
ss63 = utils.get_test_data("63.fa.sig")
sig2 = load_one_signature_from_json(ss2, ksize=31)
sig47 = load_one_signature_from_json(ss47, ksize=31)
sig63 = load_one_signature_from_json(ss63, ksize=31)
# build a fake location that matches the FakeSaveClass
# extension
fake_location = runtmp.output("out.this-is-a-test")
# this should use the plugin architecture to return an object
# of type FakeSaveClass, with the three signatures in it.
x = SaveSignaturesToLocation(fake_location)
with x as save_sig:
save_sig.add(sig2)
save_sig.add(sig47)
save_sig.add(sig63)
print(len(x))
print(x.keep)
assert isinstance(x, FakeSaveClass_HighPriority)
assert x.keep == [sig2, sig47, sig63]
assert x.priority == 1
#
# Test basic features of the save_to plugin hook.
#
class FakeCommandClass(plugins.CommandLinePlugin):
"""
A fake CLI class.
"""
command = "nifty"
description = "do somethin' nifty"
def __init__(self, parser):
super().__init__(parser)
parser.add_argument("arg1")
parser.add_argument("--other", action="store_true")
parser.add_argument("--do-fail", action="store_true")
def main(self, args):
super().main(args)
print(f"hello, world! argument is: {args.arg1}")
print(f"other is {args.other}")
if args.do_fail:
return 1
return 0
class Test_EntryPointBasics_Command:
# test the basics
def setup_method(self):
_ = plugins.get_cli_script_plugins()
self.saved_plugins = plugins._plugin_cli
plugins._plugin_cli_once = False
plugins._plugin_cli = [FakeEntryPoint("test_command", FakeCommandClass)]
def teardown_method(self):
plugins._plugin_cli = self.saved_plugins
def test_empty(self, runtmp):
# empty out script plugins...
plugins._plugin_cli = []
with pytest.raises(utils.SourmashCommandFailed):
runtmp.sourmash("scripts")
out = runtmp.last_result.out
err = runtmp.last_result.err
print(out)
print(err)
assert "(No script plugins detected!)" in out
def test_cmd_0(self, runtmp):
# test default output with some plugins
with pytest.raises(utils.SourmashCommandFailed):
runtmp.sourmash("scripts")
out = runtmp.last_result.out
err = runtmp.last_result.err
print(out)
print(err)
assert "do somethin' nifty" in out
assert "sourmash scripts nifty" in out
def test_cmd_1(self):
# test descriptions
ps = list(plugins.get_cli_scripts_descriptions())
print(ps)
assert len(ps) == 1
descr0 = ps[0]
assert "do somethin' nifty" in descr0
assert "sourmash scripts nifty" in descr0
def test_cmd_2(self):
# test get_cli_script_plugins function
ps = list(plugins.get_cli_script_plugins())
print(ps)
assert len(ps) == 1
def test_cmd_3(self, runtmp):
# test ability to run 'nifty' ;)
with pytest.raises(utils.SourmashCommandFailed):
runtmp.sourmash("scripts", "nifty")
out = runtmp.last_result.out
err = runtmp.last_result.err
print(out)
print(err)
assert "nifty: error: the following arguments are required: arg1" in err
assert "usage: nifty [-h] [-q] [-d] [--other] [--do-fail] arg1" in err
def test_cmd_4(self, runtmp):
# test basic argument parsing etc
runtmp.sourmash("scripts", "nifty", "--other", "some arg")
out = runtmp.last_result.out
err = runtmp.last_result.err
print(out)
print(err)
assert "other is True" in out
assert "hello, world! argument is: some arg" in out
def test_cmd_5(self, runtmp):
# test exit code passthru
with pytest.raises(utils.SourmashCommandFailed):
runtmp.sourmash("scripts", "nifty", "--do-fail", "some arg")
status = runtmp.last_result.status
out = runtmp.last_result.out
err = runtmp.last_result.err
print(out)
print(err)
print(status)
assert "other is False" in out
assert "hello, world! argument is: some arg" in out
class FakeCommandClass_Second(plugins.CommandLinePlugin):
"""
A fake CLI class.
"""
command = "more_nifty"
description = "do somethin' else nifty"
def __init__(self, parser):
super().__init__(parser)
parser.add_argument("arg1")
parser.add_argument("--other", action="store_true")
parser.add_argument("--do-fail", action="store_true")
def main(self, args):
super().main(args)
print(f"hello, world! argument is: {args.arg1}")
print(f"other is {args.other}")
if args.do_fail:
return 1
return 0
class FakeCommandClass_Broken_1:
"""
A fake CLI class.
"""
# command = 'more_nifty' # no command
def __init__(self, parser):
assert 0
def main(self, args):
assert 0
class FakeCommandClass_Broken_2:
"""
A fake CLI class.
"""
command = "broken"
# no description
def __init__(self, parser):
pass
def main(self, args):
return 0
class Test_EntryPointBasics_TwoCommands:
# test a second command
def setup_method(self):
_ = plugins.get_cli_script_plugins()
self.saved_plugins = plugins._plugin_cli
plugins._plugin_cli_once = False
plugins._plugin_cli = [
FakeEntryPoint("test_command", FakeCommandClass),
FakeEntryPoint("test_command2", FakeCommandClass_Second),
FakeEntryPoint("test_command3", FakeCommandClass_Broken_1),
FakeEntryPoint("test_command4", FakeCommandClass_Broken_2),
FakeEntryPoint(
"error-on-import", FakeCommandClass, error_on_import=ModuleNotFoundError
),
]
def teardown_method(self):
plugins._plugin_cli = self.saved_plugins
def test_cmd_0(self, runtmp):
# test default output for a few plugins
with pytest.raises(utils.SourmashCommandFailed):
runtmp.sourmash("scripts")
out = runtmp.last_result.out
err = runtmp.last_result.err
print(out)
print(err)
assert "do somethin' nifty" in out
assert "sourmash scripts nifty" in out
assert "do somethin' else nifty" in out
assert "sourmash scripts more_nifty" in out
def test_cmd_1(self, runtmp):
# test 'nifty'
runtmp.sourmash("scripts", "nifty", "some arg")
status = runtmp.last_result.status
out = runtmp.last_result.out
err = runtmp.last_result.err
print(out)
print(err)
print(status)
assert "other is False" in out
assert "hello, world! argument is: some arg" in out
def test_cmd_2(self, runtmp):
# test 'more_nifty'
runtmp.sourmash("scripts", "more_nifty", "some arg")
status = runtmp.last_result.status
out = runtmp.last_result.out
err = runtmp.last_result.err
print(out)
print(err)
print(status)
assert "other is False" in out
assert "hello, world! argument is: some arg" in out
def test_sourmash_info(self, runtmp):
# test 'sourmash info -v' => shows the plugins
runtmp.sourmash("info", "-v")
out = runtmp.last_result.out
err = runtmp.last_result.err
print(out)
print(err)
expected = """
groupfoo test_plugin_framework 0.1 test_command
groupfoo test_plugin_framework 0.1 test_command2
groupfoo test_plugin_framework 0.1 test_command3
groupfoo test_plugin_framework 0.1 test_command4
""".splitlines()
for line in expected:
assert line in err
def test_cli_scripts_getattr_fail():
# test scripts.__getattr__ w/fail
from sourmash.cli import scripts
with pytest.raises(AttributeError):
scripts.ThisAttrDoesNotExist
def test_cli_scripts_getattr_succ():
# test scripts.__getattr__ w/success
from sourmash.cli import scripts
scripts.subparser
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