def test_alignment_edges(monkeypatch, sb_resources):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
shutil.copy(
"{0}{1}mock_resources{1}test_muscle{1}result".format(
RES_PATH, os.path.sep), "%s%s" % (mock_tmp_dir.path, os.path.sep))
monkeypatch.setattr(Alb, "which", lambda *_: True)
monkeypatch.setattr(Alb, "Popen", MockPopen)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
# Weird binary given, but muscle found
tester = sb_resources.get_one("d f")
with pytest.raises(br.GuessError) as err:
tester = Alb.generate_msa(tester, "my_mucsle")
assert "Could not determine format from raw input" in str(err)
with pytest.raises(AttributeError) as err:
Alb.generate_msa(tester, "foo")
assert "foo is not a supported alignment tool." in str(err)
monkeypatch.setattr(br, "ask", lambda *_: False)
tmp_dir.subdir("keep_files")
with pytest.raises(SystemExit):
Alb.generate_msa(tester,
"mafft",
keep_temp="%s%skeep_files" %
(tmp_dir.path, os.path.sep))
def test_muscle(sb_resources, hf, monkeypatch):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
shutil.copy("{0}mock_resources{1}test_muscle{1}result".format(RES_PATH, os.path.sep),
"%s%s" % (mock_tmp_dir.path, os.path.sep))
monkeypatch.setattr(Alb, "which", lambda *_: True)
monkeypatch.setattr(Alb, "Popen", MockPopen)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
# basic
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'muscle')
assert hf.buddy2hash(tester) == "5ec18f3e0c9f5cf96944a1abb130232f", tester.write("temp.del")
# quiet
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'muscle', quiet=True)
assert hf.buddy2hash(tester) == "5ec18f3e0c9f5cf96944a1abb130232f", tester.write("temp.del")
# keep
monkeypatch.setattr(Sb, "hash_ids", mock_hash_ids)
tester = sb_resources.get_one("d f")
Alb.generate_msa(tester, 'muscle', keep_temp="%s%skeep_files" % (tmp_dir.path, os.path.sep))
root, dirs, files = next(os.walk("%s%skeep_files" % (tmp_dir.path, os.path.sep)))
kept_output = ""
for file in sorted(files):
with open("%s%s%s" % (root, os.path.sep, file), "r", encoding="utf-8") as ifile:
kept_output += ifile.read()
assert hf.string2hash(kept_output) == "bd85c34b11261aef2d38c7a6a9d20bf9"
def test_generate_tree_edges(alb_resources, monkeypatch):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
for root, dirs, files in os.walk("%smock_resources%stest_fasttree_inputs" % (RES_PATH, os.path.sep)):
for _file in files:
shutil.copyfile("%s%s%s" % (root, os.path.sep, _file), "%s%s%s" % (mock_tmp_dir.path, os.path.sep, _file))
monkeypatch.setattr(Pb.shutil, "which", lambda *_: True)
monkeypatch.setattr(Pb, "Popen", MockPopen)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
with pytest.raises(RuntimeError) as err:
Pb.generate_tree(alb_resources.get_one("o d n"), 'fasttree', "--nonsense")
assert "fasttree threw an error. Scroll up for more info." in str(err)
with pytest.raises(FileExistsError) as err:
Pb.generate_tree(alb_resources.get_one("o d n"), 'raxml', keep_temp=tmp_dir.path)
assert "Execution of raxml was halted to prevent files in" in str(err)
with pytest.raises(FileNotFoundError) as err:
Pb.generate_tree(alb_resources.get_one("o d n"), 'Foo')
assert 'Foo failed to generate a tree' in str(err)
monkeypatch.setattr(Pb.shutil, "which", lambda *_: None)
with pytest.raises(ProcessLookupError) as err:
Pb.generate_tree(alb_resources.get_one("o d n"), 'Foo')
assert "ProcessLookupError: #### Could not find Foo on your system. ####" in str(err)
monkeypatch.setattr(Pb.Popen, "communicate", lambda *_: ["".encode(), "".encode()])
with pytest.raises(AttributeError) as err:
Pb.generate_tree(alb_resources.get_one("o d n"), 'Foo')
assert "Foo is not a recognized tree inference tool. Please check your spelling (case sensitive)" in str(err)
def test_mafft(sb_resources, hf, monkeypatch):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
tmp_dir.subdir("keep_files")
shutil.copy("{0}{1}mock_resources{1}test_mafft{1}result".format(RES_PATH, os.path.sep),
"%s%s" % (mock_tmp_dir.path, os.path.sep))
monkeypatch.setattr(Alb, "which", lambda *_: True)
monkeypatch.setattr(Alb, "Popen", MockPopen)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
# basic
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'mafft')
assert hf.buddy2hash(tester) == "f94e0fd591dad83bd94201f0af038904", tester.write("temp.del")
# quiet
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'mafft', quiet=True)
assert hf.buddy2hash(tester) == "f94e0fd591dad83bd94201f0af038904", tester.write("temp.del")
# keep
monkeypatch.setattr(Sb, "hash_ids", mock_hash_ids)
monkeypatch.setattr(br, "ask", lambda *_: True)
tester = sb_resources.get_one("d f")
Alb.generate_msa(tester, 'mafft', keep_temp="%s%skeep_files" % (tmp_dir.path, os.path.sep))
root, dirs, files = next(os.walk("%s%skeep_files" % (tmp_dir.path, os.path.sep)))
kept_output = ""
for file in sorted(files):
with open("%s%s%s" % (root, os.path.sep, file), "r", encoding="utf-8") as ifile:
kept_output += ifile.read()
assert hf.string2hash(kept_output) == "6eaa7e087dd42a8d3ffe86d216b917d8"
def test_fasttree(alb_resources, hf, monkeypatch):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
for root, dirs, files in os.walk("%smock_resources%stest_fasttree_inputs" %
(RES_PATH, os.path.sep)):
for _file in files:
shutil.copyfile("%s%s%s" % (root, os.path.sep, _file),
"%s%s%s" % (mock_tmp_dir.path, os.path.sep, _file))
monkeypatch.setattr(Pb.shutil, "which", lambda *_: True)
monkeypatch.setattr(Pb, "Popen", MockPopen)
monkeypatch.setattr(Pb, "check_output", mock_check_output)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
# basic
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'fasttree')
assert hf.buddy2hash(
tester) == "4b2ab8c39f27b9871f9a370ca7d0c4b3", tester.write("temp.del")
# quiet
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'fasttree', quiet=True)
assert hf.buddy2hash(
tester) == "4b2ab8c39f27b9871f9a370ca7d0c4b3", tester.write("temp.del")
# params
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'fasttree', "-pseudo", quiet=True)
assert hf.buddy2hash(
tester) == "4b2ab8c39f27b9871f9a370ca7d0c4b3", tester.write("temp.del")
# slight edges
tester = alb_resources.get_one("m p s")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'fasttree-foo', quiet=True)
assert hf.buddy2hash(
tester) == "7692ee7edb8df4f91d2bdca6c3767796", tester.write("temp.del")
# keep
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
Pb.generate_tree(tester,
'fasttree',
keep_temp="%s%skeep_files" % (tmp_dir.path, os.path.sep))
root, dirs, files = next(
os.walk("%s%skeep_files" % (tmp_dir.path, os.path.sep)))
kept_output = ""
for file in sorted(files):
with open("%s%s%s" % (root, os.path.sep, file), "r") as ifile:
kept_output += ifile.read()
if os.name == "nt":
assert hf.string2hash(
kept_output) == "bcd034f0db63a7b41f4b3b6661200ef3"
else:
assert hf.string2hash(
kept_output) == "10df99cd1696b002f841aa18b78477ca"
def test_phyml(alb_resources, hf, monkeypatch):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
for root, dirs, files in os.walk("%smock_resources%stest_phyml_inputs" %
(RES_PATH, os.path.sep)):
for _file in files:
shutil.copyfile("%s%s%s" % (root, os.path.sep, _file),
"%s%s%s" % (mock_tmp_dir.path, os.path.sep, _file))
monkeypatch.setattr(Pb.shutil, "which", lambda *_: True)
monkeypatch.setattr(Pb, "Popen", MockPopen)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
# basic
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'phyml')
assert hf.buddy2hash(
tester) == "9fbcfe1d565b9fd23e2c5fca86019f8e", tester.write("temp.del")
# quiet
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'phyml', quiet=True)
assert hf.buddy2hash(
tester) == "9fbcfe1d565b9fd23e2c5fca86019f8e", tester.write("temp.del")
# params
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'phyml', "--sequential", quiet=True)
assert hf.buddy2hash(
tester) == "9fbcfe1d565b9fd23e2c5fca86019f8e", tester.write("temp.del")
# slight edges
tester = alb_resources.get_one("o p n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'phyml-foo', tmp_dir.path, quiet=True)
assert hf.buddy2hash(
tester) == "9fbcfe1d565b9fd23e2c5fca86019f8e", tester.write("temp.del")
# keep
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
Pb.generate_tree(tester,
'phyml',
keep_temp="%s%skeep_files" % (tmp_dir.path, os.path.sep))
root, dirs, files = next(
os.walk("%s%skeep_files" % (tmp_dir.path, os.path.sep)))
kept_output = ""
for file in sorted(files):
with open("%s%s%s" % (root, os.path.sep, file), "r") as ifile:
kept_output += ifile.read()
if os.name == "nt":
assert hf.string2hash(
kept_output) == "a795da6869c5e3a34962a52ec35006ed"
else:
assert hf.string2hash(
kept_output) == "5a3559c264cb4c4779f15a515aaf2286"
def test_clustalomega(sb_resources, hf, monkeypatch):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
shutil.copy(
"{1}mock_resources{0}test_clustalo{0}result".format(
os.path.sep, RES_PATH), "%s%s" % (mock_tmp_dir.path, os.path.sep))
monkeypatch.setattr(Alb, "which", lambda *_: True)
monkeypatch.setattr(Alb, "Popen", MockPopen)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
# basic
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'clustalomega')
assert hf.buddy2hash(
tester) == "f5afdc7c76ab822bdc95230329766aba", tester.write("temp.del")
# quiet
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'clustalomega', quiet=True)
assert hf.buddy2hash(
tester) == "f5afdc7c76ab822bdc95230329766aba", tester.write("temp.del")
# params
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester,
'clustalomega',
"--outfmt=nexus",
quiet=True)
assert hf.buddy2hash(
tester) == "23d7c9fa33454ed551a5896e532cf552", tester.write("temp.del")
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester,
'clustalomega',
"--outfmt=foobar",
quiet=True)
assert hf.buddy2hash(
tester) == "f5afdc7c76ab822bdc95230329766aba", tester.write("temp.del")
# keep
monkeypatch.setattr(Sb, "hash_ids", mock_hash_ids)
tester = sb_resources.get_one("d f")
Alb.generate_msa(tester,
'clustalomega',
keep_temp="%s%skeep_files" % (tmp_dir.path, os.path.sep))
root, dirs, files = next(
os.walk("%s%skeep_files" % (tmp_dir.path, os.path.sep)))
kept_output = ""
for file in sorted(files):
with open("%s%s%s" % (root, os.path.sep, file), "r",
encoding="utf-8") as ifile:
kept_output += ifile.read()
assert hf.string2hash(kept_output) == "bad3a345e769d32672d39ee51df295f5"
def test_clustalw2(sb_resources, hf, monkeypatch):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
shutil.copy(
"{1}mock_resources{0}test_clustalw2{0}result".format(
os.path.sep, hf.resource_path),
"%s%s" % (mock_tmp_dir.path, os.path.sep))
monkeypatch.setattr(Alb, "which", lambda *_: True)
monkeypatch.setattr(Alb, "Popen", MockPopen)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
# basic
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'clustalw2')
assert hf.buddy2hash(
tester) == "955440b5139c8e6d7d3843b7acab8446", tester.write("temp.del")
# quiet
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'clustalw2', quiet=True)
assert hf.buddy2hash(
tester) == "955440b5139c8e6d7d3843b7acab8446", tester.write("temp.del")
# params
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'clustalw2', "-output=nexus", quiet=True)
assert hf.buddy2hash(
tester) == "f4a61a8c2d08a1d84a736231a4035e2e", tester.write("temp.del")
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester,
'clustalw2',
"-output=foobar",
quiet=True)
assert hf.buddy2hash(
tester) == "955440b5139c8e6d7d3843b7acab8446", tester.write("temp.del")
# keep
monkeypatch.setattr(Sb, "hash_ids", mock_hash_ids)
tester = sb_resources.get_one("d f")
Alb.generate_msa(tester,
'clustalw2',
keep_temp="%s%skeep_files" % (tmp_dir.path, os.path.sep))
root, dirs, files = next(
os.walk("%s%skeep_files" % (tmp_dir.path, os.path.sep)))
kept_output = ""
for file in sorted(files):
with open("%s%s%s" % (root, os.path.sep, file), "r",
encoding="utf-8") as ifile:
kept_output += ifile.read()
assert hf.string2hash(kept_output) == "7c03d671198d4e6c4bb56c8fb5619fff"
def test_pagan(sb_resources, hf, monkeypatch):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
shutil.copy(
"{0}{1}mock_resources{1}test_pagan{1}result.fas".format(
RES_PATH, os.path.sep), "%s%s" % (mock_tmp_dir.path, os.path.sep))
open("warnings", "w").close()
assert os.path.isfile("warnings")
monkeypatch.setattr(Alb, "which", lambda *_: True)
monkeypatch.setattr(Alb, "Popen", MockPopen)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
# basic
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'pagan')
assert hf.buddy2hash(tester) == "da1c6bb365e2da8cb4e7fad32d7dafdb"
assert not os.path.isfile("warnings")
# quiet
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'pagan', quiet=True)
assert hf.buddy2hash(tester) == "da1c6bb365e2da8cb4e7fad32d7dafdb"
# params
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'pagan', "-f nexus", quiet=True)
assert hf.buddy2hash(
tester) == "f93607e234441a2577fa7d8a387ef7ec", tester.write("temp.del")
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'pagan', "-f foobar", quiet=True)
assert hf.buddy2hash(
tester) == "da1c6bb365e2da8cb4e7fad32d7dafdb", tester.write("temp.del")
# keep
monkeypatch.setattr(Sb, "hash_ids", mock_hash_ids)
tester = sb_resources.get_one("d f")
Alb.generate_msa(tester,
'pagan',
keep_temp="%s%skeep_files" % (tmp_dir.path, os.path.sep))
root, dirs, files = next(
os.walk("%s%skeep_files" % (tmp_dir.path, os.path.sep)))
kept_output = ""
for file in sorted(files):
with open("%s%s%s" % (root, os.path.sep, file), "r",
encoding="utf-8") as ifile:
kept_output += ifile.read()
assert hf.string2hash(kept_output) == "864112dafb4896ba25ece7929ca0a818"
def test_fasttree_inputs(alb_resources, hf):
temp_dir = br.TempDir()
# Nucleotide
alignbuddy = alb_resources.get_one("o d n")
tester = Pb.generate_tree(Alb.make_copy(alignbuddy), 'FastTree',
'-seed 12345')
assert hf.buddy2hash(tester) in [
'd7f505182dd1a1744b45cc326096f70c', 'da8a67cae6f3f70668f7cf04060b7cd8',
'732c5e9a978cebb1cfce6af6d64950c2'
]
tester = Pb.generate_tree(alignbuddy,
'fasttree',
'-seed 12345',
quiet=True)
assert hf.buddy2hash(tester) in [
'd7f505182dd1a1744b45cc326096f70c', 'da8a67cae6f3f70668f7cf04060b7cd8',
'732c5e9a978cebb1cfce6af6d64950c2'
]
alignbuddy = alb_resources.get_one("o p n")
tester = Pb.generate_tree(alignbuddy,
'fasttree',
'-seed 12345',
keep_temp="%s%snew_dir" %
(temp_dir.path, os.sep))
assert hf.buddy2hash(tester) in [
'57eace9bdd2074297cbd2692c1f4cd38', '82d5a9d4f44fbedf29565686a7cdfcaa',
'682210ef16beedee0e9f43c05edac112'
]
def test_liveshell_append_slash_if_dir():
tmp_dir = br.TempDir()
tmp_dir.subfile("test.txt")
assert Db.LiveShell._append_slash_if_dir(
tmp_dir.path) == "%s%s" % (tmp_dir.path, os.sep)
assert Db.LiveShell._append_slash_if_dir(
tmp_dir.subfiles[0]) == tmp_dir.subfiles[0]
def test_generate_alignment_keep_temp(monkeypatch, sb_resources):
tester = sb_resources.get_one("d f")
temp_dir = br.TempDir()
temp_dir.subdir("ga_temp_files")
def ask_false(*ask_args):
if ask_args:
pass
return False
def ask_true(*ask_args):
if ask_args:
pass
return True
monkeypatch.setattr(br, "ask", ask_false)
with pytest.raises(SystemExit):
Alb.generate_msa(tester,
clustalo_bin,
keep_temp="%s%sga_temp_files" %
(temp_dir.path, os.sep))
monkeypatch.setattr(br, "ask", ask_true)
Alb.generate_msa(tester,
clustalo_bin,
keep_temp="%s%sga_temp_files" % (temp_dir.path, os.sep))
assert os.path.isfile("{0}{1}ga_temp_files{1}result".format(
temp_dir.path, os.sep))
assert os.path.isfile("{0}{1}ga_temp_files{1}tmp.fa".format(
temp_dir.path, os.sep))
def test_walklevel():
tmp_dir = br.TempDir()
tmp_dir.subdir("mydir")
tmp_dir.subdir("mydir{0}subdir".format(os.path.sep))
tmp_dir.subdir("mydir{0}subdir{0}subsubdir".format(os.path.sep))
tmp_dir.subfile("myfile.txt")
tmp_dir.subfile("mydir{0}subfile.txt".format(os.path.sep))
tmp_dir.subfile("mydir{0}subdir{0}subsubfile.txt".format(os.path.sep))
walker = br.walklevel(tmp_dir.path)
root, dirs, files = next(walker)
assert root == tmp_dir.path
assert dirs == ["mydir"]
assert files == ["myfile.txt"]
root, dirs, files = next(walker)
assert root == "%s%smydir" % (tmp_dir.path, os.path.sep)
assert dirs == ["subdir"]
assert files == ["subfile.txt"]
with pytest.raises(StopIteration):
next(walker)
walker = br.walklevel(tmp_dir.path)
counter = 0
for _ in walker:
counter += 1
assert counter == 2
walker = br.walklevel(tmp_dir.path, level=2)
counter = 0
for _ in walker:
counter += 1
assert counter == 3
def test_tempdir_save():
save_dir = br.TempDir()
save_dir.subfile("testfile")
assert save_dir.save("%s/fakedir" % save_dir.path)
assert os.path.exists("%s/fakedir" % save_dir.path)
assert os.path.exists("%s/fakedir/testfile" % save_dir.path)
assert not save_dir.save("%s/fakedir" % save_dir.path)
def test_liveshell_complete_load_save_write(monkeypatch):
monkeypatch.setattr(Db.LiveShell, "cmdloop", mock_cmdloop)
dbbuddy = Db.DbBuddy()
crash_file = br.TempFile(byte_mode=True)
liveshell = Db.LiveShell(dbbuddy, crash_file)
tmpdir = br.TempDir()
os.chdir(tmpdir.path)
tmpdir.subfile("file.txt")
tmpdir.subdir("extra_dir")
# Load
assert liveshell.complete_load("load fi ", "load fi ", 5,
7) == ['file.txt']
assert liveshell.complete_load(
"load ", "load ", 5, 5) == ['extra_dir%s' % os.path.sep, 'file.txt']
assert not liveshell.complete_load("load ", "load ", 4, 5)
# Save
assert liveshell.complete_save("save fi ", "save fi ", 5,
7) == ['file.txt']
assert liveshell.complete_save(
"save ", "save ", 5, 5) == ['extra_dir%s' % os.path.sep, 'file.txt']
assert not liveshell.complete_save("save ", "save ", 4, 5)
# Save
assert liveshell.complete_write("write fi ", "write fi ", 6,
8) == ['file.txt']
assert liveshell.complete_write(
"write ", "write ", 6, 6) == ['extra_dir%s' % os.path.sep, 'file.txt']
assert not liveshell.complete_write("write ", "write ", 4, 5)
def test_liveshell_do_bash(monkeypatch, capsys):
monkeypatch.setattr(Db.LiveShell, "cmdloop", mock_cmdloop)
dbbuddy = Db.DbBuddy()
crash_file = br.TempFile(byte_mode=True)
liveshell = Db.LiveShell(dbbuddy, crash_file)
capsys.readouterr()
tmp_file = br.TempFile()
liveshell.do_bash("echo 'hello from bash' > %s" % tmp_file.path)
assert "hello from bash" in tmp_file.read()
monkeypatch.setattr(
"builtins.input",
lambda _: "echo 'Line from input' > %s" % tmp_file.path)
liveshell.do_bash(None)
assert "Line from input" in tmp_file.read()
liveshell.do_bash("cd /this/path/doesnt/exist")
out, err = capsys.readouterr()
assert "-sh: cd: /this/path/doesnt/exist: No such file or directory\n" in out
tmp_dir = br.TempDir()
tmp_dir.subfile("foo.txt")
cwd = os.getcwd()
liveshell.do_bash("cd %s" % tmp_dir.path)
out, err = capsys.readouterr()
assert tmp_dir.path in out
assert os.path.isfile("foo.txt")
os.chdir(cwd)
def test_tempdir_make_dir_generator():
test_dir = br.TempDir()
dir_path = test_dir.path
for _ in test_dir._make_dir():
pass
assert not os.path.isdir(dir_path)
os.makedirs(dir_path)
def test_prank(sb_resources, hf, monkeypatch):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
shutil.copy(
"{0}{1}mock_resources{1}test_prank{1}result.best.fas".format(
RES_PATH, os.path.sep), "%s%s" % (mock_tmp_dir.path, os.path.sep))
monkeypatch.setattr(Alb, "which", lambda *_: True)
monkeypatch.setattr(Alb, "Popen", MockPopen)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
# basic
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'prank')
assert hf.buddy2hash(
tester) == "eff3e6728b5126e285a422863567294f", tester.write("temp.del")
# quiet
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'prank', quiet=True)
assert hf.buddy2hash(
tester) == "eff3e6728b5126e285a422863567294f", tester.write("temp.del")
# params
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'prank', "-f=nexus", quiet=True)
assert hf.buddy2hash(
tester) == "4dcaa948e109487ee12512b6ac02183c", tester.write("temp.del")
tester = sb_resources.get_one("d f")
tester = Alb.generate_msa(tester, 'prank', "-f=foobar", quiet=True)
assert hf.buddy2hash(
tester) == "eff3e6728b5126e285a422863567294f", tester.write("temp.del")
# keep
monkeypatch.setattr(Sb, "hash_ids", mock_hash_ids)
tester = sb_resources.get_one("d f")
Alb.generate_msa(tester,
'prank',
keep_temp="%s%skeep_files" % (tmp_dir.path, os.path.sep))
root, dirs, files = next(
os.walk("%s%skeep_files" % (tmp_dir.path, os.path.sep)))
kept_output = ""
for file in sorted(files):
with open("%s%s%s" % (root, os.path.sep, file), "r",
encoding="utf-8") as ifile:
kept_output += ifile.read()
assert hf.string2hash(kept_output) == "d0564931e20a61b441fc60549f5560a0"
def test_liveshell_do_write(monkeypatch, capsys, hf):
monkeypatch.setattr(Db.LiveShell, "cmdloop", mock_cmdloop)
monkeypatch.setattr(Db.LiveShell, "dump_session", lambda _: True)
dbbuddy = Db.DbBuddy()
crash_file = br.TempFile(byte_mode=True)
liveshell = Db.LiveShell(dbbuddy, crash_file)
load_file = "%s/mock_resources/test_databasebuddy_clients/dbbuddy_save.db" % hf.resource_path
liveshell.do_load(load_file)
capsys.readouterr()
tmp_dir = br.TempDir()
# write a summary
monkeypatch.setattr("builtins.input", lambda _: "%s/save1" % tmp_dir.path)
liveshell.do_write(None)
assert os.path.isfile("%s/save1" % tmp_dir.path)
with open("%s/save1" % tmp_dir.path, "r") as ifile:
assert len(ifile.read()) == 249980
out, err = capsys.readouterr()
assert re.search("1407 summary records.*written to.*save1", out)
# write ids/accns
dbbuddy.out_format = "ids"
monkeypatch.setattr(br, "ask", lambda _: True)
dbbuddy.records['O14727'].record = Db.Record('O14727', _record=True)
liveshell.do_write("%s/save2" % tmp_dir.path)
assert os.path.isfile("%s/save2" % tmp_dir.path)
with open("%s/save2" % tmp_dir.path, "r") as ifile:
assert len(ifile.read()) == 18661
out, err = capsys.readouterr()
assert re.search("1407 accessions.*written to.*save2", out)
# Abort summary
monkeypatch.setattr(br, "ask", lambda _: False)
liveshell.do_write("%s/save3" % tmp_dir.path)
assert not os.path.isfile("%s/save3" % tmp_dir.path)
out, err = capsys.readouterr()
assert "Abort..." in out
# Permission error
dbbuddy.out_format = "fasta"
monkeypatch.setattr("builtins.open", OpenPermissionError)
liveshell.do_write("%s/save4" % tmp_dir.path)
assert not os.path.isfile("%s/save4" % tmp_dir.path)
out, err = capsys.readouterr()
assert "Error: You do not have write privileges in the specified directory.\n\n" in out
# File exists
monkeypatch.setattr(br, "ask", lambda _: False)
liveshell.do_write("%s/save2" % tmp_dir.path)
out, err = capsys.readouterr()
assert "Abort..." in out
assert "written" not in out
# Not a directory
liveshell.do_write("%s/ghostdir/save5" % tmp_dir.path)
out, err = capsys.readouterr()
assert "The specified directory does not exist. Please create it before continuing" in out
assert "written" not in out
def test_write(sb_resources, hf):
temp_dir = br.TempDir()
tester = sb_resources.get_one("d g")
tester.write("%s/sequences.gb" % temp_dir.path)
with open("%s/sequences.gb" % temp_dir.path, encoding="utf-8") as ifile:
assert hf.string2hash(ifile.read()) == "2e02a8e079267bd9add3c39f759b252c"
tester.write("%s/sequences.fa" % temp_dir.path, out_format="fasta")
with open("%s/sequences.fa" % temp_dir.path, encoding="utf-8") as ifile:
assert hf.string2hash(ifile.read()) == "25073539df4a982b7f99c72dd280bb8f"
def test_setup(capsys, monkeypatch):
tmp_dir = br.TempDir()
__init__ = tmp_dir.subfile("__init__")
monkeypatch.setattr(Bs.buddysuite, "__file__", __init__)
monkeypatch.setattr(br, "ask", lambda *_: True)
monkeypatch.setattr("builtins.input", lambda *_: "")
sys.argv = ['BuddySuite.py', "-s"]
Bs.main()
assert os.path.isdir("%s/buddy_data" % tmp_dir.path)
assert os.path.isfile("%s/buddy_data/config.ini" % tmp_dir.path)
assert os.path.isfile("%s/buddy_data/buddysuite_usage.json" % tmp_dir.path)
assert os.path.isfile("%s/buddy_data/cmd_history" % tmp_dir.path)
out, err = capsys.readouterr()
assert out == """\
[1mWelcome to BuddySuite![m
Let's configure your installation:
[1mProviding a valid email address is recommended if accessing public databases with BuddySuite.
The maintainers of those resources may attempt to contact you before blocking your IP if you are not adhering to their usage limitations.[m
[1mBuddySuite is able to automatically send anonymized usage statistics and crash reports to the developers as part of the software improvement program.[m
[1mSuccess! You're all set.[m
Email address: [email protected]
Send diagnostics: True
These choices can be changed at any time by re-running setup.
Enjoy the BuddySuite!
"""
monkeypatch.setattr(br, "ask", lambda *_: False)
monkeypatch.setattr("builtins.input", lambda *_: "*****@*****.**")
Bs.main()
out, err = capsys.readouterr()
assert out == """\
[1mWelcome to BuddySuite![m
Let's configure your installation:
[1mProviding a valid email address is recommended if accessing public databases with BuddySuite.
The maintainers of those resources may attempt to contact you before blocking your IP if you are not adhering to their usage limitations.[m
[1mBuddySuite is able to automatically send anonymized usage statistics and crash reports to the developers as part of the software improvement program.[m
[1mSuccess! You're all set.[m
Email address: [email protected]
Send diagnostics: False
These choices can be changed at any time by re-running setup.
Enjoy the BuddySuite!
"""
monkeypatch.setattr("builtins.input", lambda *_: "not an email address")
Bs.main()
out, err = capsys.readouterr()
assert out == """\
def test_write(sb_resources, hf):
temp_dir = br.TempDir()
tester = sb_resources.get_one("d g")
tester.write("%s/sequences.gb" % temp_dir.path)
with open("%s/sequences.gb" % temp_dir.path, encoding="utf-8") as ifile:
assert hf.string2hash(
ifile.read()) == "2e02a8e079267bd9add3c39f759b252c"
tester.write("%s/sequences.fa" % temp_dir.path, out_format="fasta")
with open("%s/sequences.fa" % temp_dir.path, encoding="utf-8") as ifile:
data = ifile.read()
assert hf.string2hash(data) == "6a9b3b554aa9ddb90ea62967bd26d5b7"
def test_tempdir_subdirs():
test_dir = br.TempDir()
subdir = test_dir.subdir("test")
assert os.path.exists(subdir)
assert os.path.exists("{0}/test".format(test_dir.path))
with pytest.raises(ValueError):
test_dir.del_subdir("dasdfs")
test_dir.del_subdir("test")
assert not os.path.exists(subdir)
assert not os.path.exists("{0}/test".format(test_dir.path))
subdir = test_dir.subdir()
assert os.path.exists(subdir)
test_dir.del_subdir(subdir)
def test_liveshell_do_save(monkeypatch, capsys):
monkeypatch.setattr(Db.LiveShell, "cmdloop", mock_cmdloop)
dbbuddy = Db.DbBuddy()
crash_file = br.TempFile(byte_mode=True)
liveshell = Db.LiveShell(dbbuddy, crash_file)
dbbuddy.records["foo"] = "bar"
# Standard, no problems
tmp_dir = br.TempDir()
monkeypatch.setattr("builtins.input",
lambda _: "%s/save_dir/save_file1" % tmp_dir.path)
liveshell.do_save(None)
out, err = capsys.readouterr()
assert "Live session saved\n\n" in out
assert os.path.isfile("%s/save_dir/save_file1.db" % tmp_dir.path)
with open("%s/save_dir/save_file1.db" % tmp_dir.path, "rb") as ifile:
assert len(ifile.read()) in [
279, 281
] # Different versions of python give different file sizes
# File exists, abort
monkeypatch.setattr(br, "ask", lambda _, **kwargs: False)
liveshell.do_save("%s/save_dir/save_file1" % tmp_dir.path)
out, err = capsys.readouterr()
assert "Abort...\n\n" in out
# PermissionError
monkeypatch.setattr("builtins.open", OpenPermissionError)
liveshell.do_save("%s/save_dir/save_file2" % tmp_dir.path)
out, err = capsys.readouterr()
assert "Error: You do not have write privileges to create a file in the specified directory.\n\n" in out
assert not os.path.isfile("%s/save_dir/save_file2.db" % tmp_dir.path)
def makedirs_permissionerror(*args, **kwargs):
print("makedirs_permissionerror\nargs: %s\nkwargs: %s" %
(args, kwargs))
raise PermissionError
monkeypatch.setattr(os, "makedirs", makedirs_permissionerror)
liveshell.do_save("%s/save_dir/deeper_dir/save_file2" % tmp_dir.path)
out, err = capsys.readouterr()
assert "Error: You do not have write privileges to create a directory in the specified path.\n\n" in out
assert not os.path.isfile(
"%s/save_dir/deeper_dir/save_file2.db" % tmp_dir.path)
def test_liveshell_init(monkeypatch, capsys, hf):
# Default instantiate
monkeypatch.setattr(Db.LiveShell, "cmdloop", mock_cmdloop)
dbbuddy = Db.DbBuddy()
crash_file = br.TempFile(byte_mode=True)
liveshell = Db.LiveShell(dbbuddy, crash_file)
assert type(liveshell.tmpdir) == br.TempDir
assert liveshell.terminal_default == "\033[m\033[40m\033[97m"
assert liveshell.prompt == '[95m[1mDbBuddy[m[40m[97m[1m>[m[40m[97m '
assert hf.string2hash(
liveshell.doc_leader) == "e71aa4976437bdb0c22eeaacfaea6f9f"
assert hash(liveshell.dbbuddy) == hash(dbbuddy)
assert liveshell.crash_file == crash_file
assert os.path.split(liveshell.history_path)[-1] == "cmd_history"
assert not liveshell.undo
assert not liveshell.hash
assert liveshell.shell_execs == []
assert type(liveshell.usage) == br.Usage
out, err = capsys.readouterr()
assert "Your session is currently unpopulated. Use 'search' to retrieve records." in out
# Set cmd history path
tmp_dir = br.TempDir()
monkeypatch.setitem(Db.CONFIG, "data_dir", tmp_dir.path)
liveshell = Db.LiveShell(dbbuddy, crash_file)
assert liveshell.history_path == "%s%scmd_history" % (tmp_dir.path, os.sep)
# Permission error
os.chmod("%s%scmd_history" % (tmp_dir.path, os.sep), 0o333)
liveshell = Db.LiveShell(dbbuddy, crash_file)
# Windows does not actually change the permissions with os.chmod...
if os.name != "nt":
assert liveshell.history_path == "%s%scmd_history" % (
liveshell.tmpdir.path, os.sep)
# Run initial search
monkeypatch.setattr(Db, "retrieve_summary", lambda _: True)
dbbuddy = Db.DbBuddy("Inx15")
Db.LiveShell(dbbuddy, crash_file)
assert not dbbuddy.records
Db.LiveShell(dbbuddy, crash_file)
dbbuddy = Db.DbBuddy("ENSAMEG00000011912")
assert len(dbbuddy.records) == 1
def test_inplace(capsys, alb_resources, hf):
tmp_dir = br.TempDir()
tester = alb_resources.get_one("o d f")
tester.write("%s/align" % tmp_dir.path)
test_in_args = deepcopy(in_args)
test_in_args.transcribe = True
test_in_args.in_place = True
test_in_args.alignments = ["%s/align" % tmp_dir.path]
Alb.command_line_ui(test_in_args, tester, skip_exit=True)
out, err = capsys.readouterr()
tester = Alb.AlignBuddy("%s/align" % tmp_dir.path)
assert "File over-written at:" in err
assert hf.buddy2hash(tester) == "8f78e0c99e2d6d7d9b89b8d854e02bcd", tester.write("temp.del")
test_in_args.alignments = ["I/do/not/exist"]
Alb.command_line_ui(test_in_args, alb_resources.get_one("o d f"), skip_exit=True)
out, err = capsys.readouterr()
assert "Warning: The -i flag was passed in, but the positional argument doesn't seem to be a file." in err
def test_uninstall(monkeypatch):
tmp_dir = br.TempDir()
tmp_dir.subdir("main_site")
tmp_dir.subdir("main_site/buddysuite")
__init__ = tmp_dir.subfile("main_site/buddysuite/__init__")
monkeypatch.setattr(Bs.buddysuite, "__file__", __init__)
tmp_dir.subfile("seqbuddy")
tmp_dir.subfile("alignbuddy")
tmp_dir.subfile("databasebuddy")
tmp_dir.subfile("phylobuddy")
tmp_dir.subfile("sb")
tmp_dir.subfile("something_else")
monkeypatch.setattr(br, "ask", lambda *_, **__: True)
monkeypatch.setattr(
br, "config_values",
lambda *_: {"shortcuts": ["/not/a/link",
"%s/sb" % tmp_dir.path]})
monkeypatch.setattr(shutil, "which", lambda buddy: "%s/%s" %
(tmp_dir.path, buddy))
sys.argv = ['BuddySuite.py', "-u"]
root, dirs, files = next(br.walklevel(tmp_dir.path))
assert dirs == ["main_site"]
assert sorted(files) == [
'alignbuddy', 'databasebuddy', 'phylobuddy', 'sb', 'seqbuddy',
'something_else'
]
Bs.main()
root, dirs, files = next(br.walklevel(tmp_dir.path))
assert dirs == []
assert files == ["something_else"]
# Run one more time to ensure that the rmtree FileNotFoundError raises
Bs.main()
root, dirs, files = next(br.walklevel(tmp_dir.path))
assert dirs == []
assert files == ["something_else"]
def test_tempdir_subfiles():
test_dir = br.TempDir()
subfile = test_dir.subfile("testfile")
assert os.path.exists(subfile)
assert os.path.exists("{0}/testfile".format(test_dir.path))
with open(subfile, 'w') as file_to_write:
file_to_write.write("hello world")
with open(subfile, 'r') as file_to_write:
assert file_to_write.read() == "hello world"
with open("{0}/testfile".format(test_dir.path), 'r') as file_to_write:
assert file_to_write.read() == "hello world"
with pytest.raises(ValueError):
test_dir.del_subfile("dasdfs")
test_dir.del_subfile("testfile")
assert not os.path.exists(subfile)
assert not os.path.exists("{0}/testfile".format(test_dir.path))
subfile = test_dir.subfile()
assert os.path.exists(subfile)
test_dir.del_subfile(subfile)
def test_tempdir_init():
test_dir = br.TempDir()
assert os.path.exists(test_dir.path)
assert not len(test_dir.subdirs)
assert not len(test_dir.subfiles)
import urllib.request
import argparse
import json
from hashlib import md5
from time import sleep
import datetime
from unittest import mock
import AlignBuddy as Alb
import buddy_resources as br
from pkg_resources import DistributionNotFound
from configparser import ConfigParser
if os.name == "nt":
import msvcrt
# Globals
TEMP_DIR = br.TempDir()
RESOURCE_PATH = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'..{0}unit_test_resources{0}'.format(os.path.sep))
# Mock resources
class MockLocation(object):
def __init__(self):
self.start = 0
self.end = 1
def mock_valueerror(*args, **kwargs):
raise ValueError(args, kwargs)
