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 mock_urlopen_uniprot_summary(*args, **kwargs):
print("mock_urlopen_uniprot_summary\nargs: %s\nkwargs: %s" %
(args, kwargs))
tmp_file = br.TempFile(byte_mode=True)
tmp_file.write('''# Search: inx15
A8XEF9 A8XEF9_CAEBR 381 6238 Caenorhabditis briggsae Innexin Function (1); Sequence similarities (1); \
Subcellular location (2)
O61786 O61786_CAEEL 382 6239 Caenorhabditis elegans Innexin Function (1); Sequence similarities (1); \
Subcellular location (2)
A0A0H5SBJ0 A0A0H5SBJ0_BRUMA 129 6279 Brugia malayi (Filarial nematode worm) Innexin Function (1); Sequence \
similarities (1); Subcellular location (1)
E3MGD6 E3MGD6_CAERE 384 31234 Caenorhabditis remanei (Caenorhabditis vulgaris) Innexin Function (1); Sequence \
similarities (1); Subcellular location (2)
//
# Search: inx16
O61787 INX16_CAEEL 372 6239 Caenorhabditis elegans Innexin-16 (Protein opu-16) Function (1); Sequence \
similarities (1); Subcellular location (1)
A0A0V1AZ11 A0A0V1AZ11_TRISP 406 6334 Trichinella spiralis (Trichina worm) Innexin Caution (1); Function (1); \
Sequence similarities (1); Subcellular location (2)
A8XEF8 A8XEF8_CAEBR 374 6238 Caenorhabditis briggsae Innexin Function (1); Sequence similarities (1); \
Subcellular location (2)
A0A0B2VB60 A0A0B2VB60_TOXCA 366 6265 Toxocara canis (Canine roundworm) Innexin Caution (2); Function (1); \
Sequence similarities (1); Subcellular location (1)
A0A0V0W5E2 A0A0V0W5E2_9BILA 410 92179 Trichinella sp. T6 Innexin Caution (2); Function (1); Sequence \
similarities (1); Subcellular location (1)
//'''.encode("utf-8"))
return tmp_file.get_handle("r")
def test_screw_formats_inplace_ui(capsys, pb_odd_resources):
temp_file = br.TempFile()
with open(pb_odd_resources["compare"], "r") as ifile:
temp_file.write(ifile.read())
test_in_args = deepcopy(in_args)
test_in_args.screw_formats = "nexus"
test_in_args.in_place = True
test_in_args.trees[0] = temp_file.path
tester = Pb.PhyloBuddy(temp_file.path)
Pb.command_line_ui(test_in_args, tester, skip_exit=True)
out, err = capsys.readouterr()
assert "File overwritten at:" in err
check_file = os.path.isfile("%s.nex" % temp_file.path)
assert check_file
test_in_args.trees[0] = "%s.nex" % temp_file.path
test_in_args.screw_formats = "newick"
tester = Pb.PhyloBuddy("%s.nex" % temp_file.path)
Pb.command_line_ui(test_in_args, tester, skip_exit=True)
out, err = capsys.readouterr()
assert "File overwritten at:" in err
check_file = os.path.isfile("%s.nwk" % temp_file.path)
assert check_file
def test_write2(alb_resources, hf, key, next_hash):
temp_file = br.TempFile()
alignbuddy = alb_resources.get_one(key)
alignbuddy.write(temp_file.path, out_format="phylipr")
with open(temp_file.path, "r", encoding="utf-8") as ifile:
tester_hash = hf.string2hash(ifile.read())
assert tester_hash == next_hash
def test_liveshell_do_fetch(monkeypatch, capsys):
def mock_big_record_no_dl(_dbbuddy):
_dbbuddy.records["NP_001287575.1"] = Db.Record("NP_001287575.1",
_size=5000001)
def mock_big_record_fetch(_dbbuddy):
_dbbuddy.records["NP_001287575.1"].record = True
monkeypatch.setattr(Db.LiveShell, "cmdloop", mock_cmdloop)
monkeypatch.setattr(Db.LiveShell, "dump_session", lambda _: True)
monkeypatch.setattr(Db, "retrieve_summary", lambda _: True)
dbbuddy = Db.DbBuddy("NP_001287575.1")
crash_file = br.TempFile(byte_mode=True)
liveshell = Db.LiveShell(dbbuddy, crash_file)
monkeypatch.setattr(Db, "retrieve_summary", mock_big_record_no_dl)
monkeypatch.setattr(br, "ask", lambda _, **kwargs: False)
liveshell.do_fetch("Foo")
assert dbbuddy.records["NP_001287575.1"].size == 5000001
out, err = capsys.readouterr()
assert "Aborted...\n\n" in out
monkeypatch.setattr(Db, "retrieve_sequences", mock_big_record_fetch)
monkeypatch.setattr(br, "ask", lambda _, **kwargs: True)
liveshell.do_fetch(None)
out, err = capsys.readouterr()
print(out)
assert "Retrieved 5.0 M residues of sequence data\n\n" in out
def test_liveshell_do_search(monkeypatch):
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)
dbbuddy.search_terms += ["Foo", "Bar"]
monkeypatch.setattr("builtins.input", lambda _: "Panx1, Panx2")
monkeypatch.setattr(Db, "retrieve_summary", lambda _: True)
liveshell.do_search(None)
assert dbbuddy.search_terms == ["Foo", "Bar", "Panx1", "Panx2"]
assert not dbbuddy.records
assert not dbbuddy.failures
mock_buddy = Db.DbBuddy("Cx43, Cx32")
mock_buddy.records["NewRec1"] = True
mock_buddy.failures["NewFailure1"] = True
monkeypatch.setattr(Db, "DbBuddy", lambda _: mock_buddy)
liveshell.do_search("Blahh")
assert dbbuddy.search_terms == [
"Foo", "Bar", "Panx1", "Panx2", "Cx43", "Cx32"
]
assert "NewRec1" in dbbuddy.records
assert "NewFailure1" in dbbuddy.failures
def test_delete_records_ui(capsys, alb_resources, hf):
test_in_args = deepcopy(in_args)
test_in_args.delete_records = ["α[1-5]", "β[A-M]"]
Alb.command_line_ui(test_in_args, alb_resources.get_one("m d s"), skip_exit=True)
out, err = capsys.readouterr()
assert hf.string2hash(out) == "de5beddbc7f0a7f8e3dc2d5fd43b7b29"
assert hf.string2hash(err) == "31bb4310333851964015e21562f602c2"
test_in_args.delete_records = ["α[1-5]", "β[A-M]", 4]
Alb.command_line_ui(test_in_args, alb_resources.get_one("m d s"), skip_exit=True)
out, err = capsys.readouterr()
assert hf.string2hash(err) == "ce6c9b29c95ba853eb444de5c71aeca9"
test_in_args.delete_records = ["foo"]
Alb.command_line_ui(test_in_args, alb_resources.get_one("m d s"), skip_exit=True)
out, err = capsys.readouterr()
assert "No sequence identifiers match 'foo'\n" in err
tmp_file = br.TempFile()
with open(tmp_file.path, "w", encoding="utf-8") as ofile:
ofile.write('''\
α[1-5]
β[A-M]
''')
test_in_args.delete_records = [tmp_file.path]
Alb.command_line_ui(test_in_args, alb_resources.get_one("m d s"), skip_exit=True)
out, err = capsys.readouterr()
assert hf.string2hash(out) == "de5beddbc7f0a7f8e3dc2d5fd43b7b29"
def test_instantiate_dbbuddy_from_handle():
tmp_file = br.TempFile()
tmp_file.write(", ".join(ACCNS))
tmp_file.open("r")
dbbuddy = Db.DbBuddy(tmp_file.handle)
for accn in ACCNS:
assert accn in dbbuddy.records
def test_liveshell_postcmd(monkeypatch):
monkeypatch.setattr(Db.LiveShell, "cmdloop", mock_cmdloop)
dbbuddy = Db.DbBuddy()
crash_file = br.TempFile(byte_mode=True)
liveshell = Db.LiveShell(dbbuddy, crash_file)
assert liveshell.postcmd("STOP!", "foo bar line") == "STOP!"
assert liveshell.usage.stats['LiveShell'][Db.VERSION.short()]['foo'] == 1
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_config_values(monkeypatch):
fake_config = br.TempFile()
fake_config.write(
"[DEFAULT]\nuser_hash = ABCDEFG\ndiagnostics = True\nemail = [email protected]"
"\nshortcuts = /usr/local/sb,/usr/local/alb")
fake_config.close()
config_path = fake_config.path
monkeypatch.setattr(br, "resource_filename", lambda *_: config_path)
options = br.config_values()
assert options["user_hash"] == "ABCDEFG"
assert options["diagnostics"]
assert options["email"] == "*****@*****.**"
assert options["shortcuts"] == ['/usr/local/sb', '/usr/local/alb']
def mock_keyerror(*args, **kwargs):
raise KeyError(args, kwargs)
monkeypatch.setattr(ConfigParser, "getboolean", mock_keyerror)
monkeypatch.setattr(ConfigParser, "get", mock_keyerror)
options = br.config_values()
assert options["user_hash"] == "hashless"
assert not options["diagnostics"]
assert options["email"] == "*****@*****.**"
def mock_distributionerror(*args, **kwargs):
raise DistributionNotFound(args, kwargs)
monkeypatch.setattr(br, "resource_filename", mock_distributionerror)
options = br.config_values()
assert not options["data_dir"]
def test_liveshell_do_database(monkeypatch, capsys):
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)
liveshell.do_database("'NcBi_nuc',\t \"ENSEMBl,uniprot")
assert sorted(dbbuddy.databases) == ['ensembl', 'ncbi_nuc', 'uniprot']
liveshell.do_database("ensembl,all")
assert sorted(
dbbuddy.databases) == ["ensembl", "ncbi_nuc", "ncbi_prot", "uniprot"]
capsys.readouterr()
liveshell.do_database("Foo ensembl")
out, err = capsys.readouterr()
assert "Invalid database choice(s): foo." in out
assert dbbuddy.databases == ['ensembl']
liveshell.do_database("Foo")
out, err = capsys.readouterr()
assert "Database search list not changed." in out
assert dbbuddy.databases == ['ensembl']
monkeypatch.setattr("builtins.input", lambda _: "'ncbi_nuc', 'ensembl'")
liveshell.do_database(None)
assert sorted(dbbuddy.databases) == ['ensembl', 'ncbi_nuc']
def test_liveshell_complete_format(monkeypatch):
monkeypatch.setattr(Db.LiveShell, "cmdloop", mock_cmdloop)
dbbuddy = Db.DbBuddy()
crash_file = br.TempFile(byte_mode=True)
liveshell = Db.LiveShell(dbbuddy, crash_file)
assert liveshell.complete_format("f") == ['full-summary', 'fasta', 'fastq', 'fastq-sanger',
'fastq-solexa', 'fastq-illumina']
def test_liveshell_do_load(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)
dbbuddy.server_clients["uniprot"] = Db.UniProtRestClient(dbbuddy)
dbbuddy.server_clients["uniprot"].http_errors_file.write("Hello!")
db_session = "%s/mock_resources/test_databasebuddy_clients/dbbuddy_save.db" % hf.resource_path
monkeypatch.setattr("builtins.input", lambda _: db_session)
liveshell.do_load(None)
out, err = capsys.readouterr()
assert "Session loaded from file.\n\n" in out
assert dbbuddy.server_clients["uniprot"].http_errors_file.read() == ""
headings = liveshell.get_headings()
for heading in ['ACCN', 'DB', 'Type', 'record', 'entry_name', 'length', 'organism-id', 'organism',
'protein_names', 'comments', 'gi_num', 'TaxId', 'status', 'name', 'biotype',
'object_type', 'strand', 'assembly_name', 'name']:
assert heading in headings
for heading in headings:
assert heading in ['ACCN', 'DB', 'Type', 'record', 'entry_name', 'length', 'organism-id', 'organism',
'protein_names', 'comments', 'gi_num', 'TaxId', 'status', 'name', 'biotype',
'object_type', 'strand', 'assembly_name', 'name']
monkeypatch.setattr("builtins.input", lambda _: "/no/file/here")
liveshell.do_load(None)
out, err = capsys.readouterr()
assert "Error: Unable to read the provided file. Are you sure it's a saved DbBuddy live session?\n\n" in out
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 mock_urlopen_handle_uniprot_ids(*args, **kwargs):
print("mock_urlopen_handle_uniprot_ids\nargs: %s\nkwargs: %s" % (args, kwargs))
tmp_file = br.TempFile(byte_mode=True)
tmp_file.write('''A8XEF9
O61786
A0A0H5SBJ0
'''.encode("utf-8"))
return tmp_file.get_handle("r")
def test_liveshell_complete_database(monkeypatch):
monkeypatch.setattr(Db.LiveShell, "cmdloop", mock_cmdloop)
dbbuddy = Db.DbBuddy()
crash_file = br.TempFile(byte_mode=True)
liveshell = Db.LiveShell(dbbuddy, crash_file)
assert sorted(liveshell.complete_database("")) == [
'ensembl', 'ncbi_nuc', 'ncbi_prot', 'uniprot'
]
def test_liveshell_get_headings(monkeypatch):
monkeypatch.setattr(Db.LiveShell, "cmdloop", mock_cmdloop)
monkeypatch.setattr(Db, "retrieve_summary", lambda _: True)
dbbuddy = Db.DbBuddy(",".join(ACCNS))
crash_file = br.TempFile(byte_mode=True)
liveshell = Db.LiveShell(dbbuddy, crash_file)
dbbuddy.records['XM_003978475'].summary = {'organism': 'velociraptor'}
assert liveshell.get_headings() == ['ACCN', 'DB', 'Type', 'record', 'organism']
def test_liveshell_complete_delete(monkeypatch):
monkeypatch.setattr(Db.LiveShell, "cmdloop", mock_cmdloop)
dbbuddy = Db.DbBuddy()
crash_file = br.TempFile(byte_mode=True)
liveshell = Db.LiveShell(dbbuddy, crash_file)
assert liveshell.complete_delete("") == [
"all", "failures", "search", "trash", "records"
]
def test_write1(alb_resources, hf, key, next_hash):
temp_file = br.TempFile()
alignbuddy = alb_resources.get_one(key)
alignbuddy.write(temp_file.path)
with open(temp_file.path, "r", encoding="utf-8") as ifile:
output = ifile.read()
tester_hash = hf.string2hash(output)
assert tester_hash == next_hash
def test_liveshell_do_restore(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)
monkeypatch.setattr(Db.LiveShell, "filter", mock_filter)
liveshell.do_restore(None)
out, err = capsys.readouterr()
assert "'restore' filter mocked! None" in out
def patch_ensembl_perform_rest_action(*args, **kwargs):
print("patch_ensembl_perform_rest_action\nargs: %s\nkwargs: %s" % (args, kwargs))
if "info/species" in args:
with open("%s/ensembl_species.json" % test_files, "r") as ifile:
return json.load(ifile)
elif "sequence/id" in args:
with open("%s/ensembl_sequence.seqxml" % test_files, "r") as ifile:
tmp_file = br.TempFile(byte_mode=True)
tmp_file.write(ifile.read().encode())
return Db.SeqIO.parse(tmp_file.get_handle("r"), "seqxml")
def test_liveshell_complete_bash(monkeypatch):
# Note, this doesn't work in Windows
if os.name == "nt":
return
monkeypatch.setattr(Db.LiveShell, "cmdloop", mock_cmdloop)
dbbuddy = Db.DbBuddy()
crash_file = br.TempFile(byte_mode=True)
liveshell = Db.LiveShell(dbbuddy, crash_file)
programs = liveshell.complete_bash("wh")
for program in ['wheel ', 'whereis ', 'whoami ', 'which ', 'who ']:
assert program in programs
def test_liveshell_do_trash(monkeypatch, capsys):
def mock_show(_, line, mode):
print("%s show mocked! %s" % (mode, line))
return
monkeypatch.setattr(Db.LiveShell, "cmdloop", mock_cmdloop)
dbbuddy = Db.DbBuddy()
crash_file = br.TempFile(byte_mode=True)
liveshell = Db.LiveShell(dbbuddy, crash_file)
monkeypatch.setattr(Db.LiveShell, "do_show", mock_show)
liveshell.do_trash(None)
out, err = capsys.readouterr()
assert "trash_bin show mocked! None" in out
def test_liveshell_default(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)
liveshell.default("Dunno...")
out, err = capsys.readouterr()
assert '*** Unknown syntax: Dunno...\n\n' in out
with pytest.raises(SystemExit):
liveshell.default("exit")
out, err = capsys.readouterr()
assert "Goodbye" in out
def mock_urlopen_uniprot_count_hits(*args, **kwargs):
print("mock_urlopen_uniprot_count_hits\nargs: %s\nkwargs: %s" % (args, kwargs))
tmp_file = br.TempFile(byte_mode=True)
tmp_file.write('''# Search: (inx15)+OR+(inx16)
O61787
A0A0V1AZ11
A8XEF9
A8XEF8
A0A0B2VB60
A0A0V0W5E2
O61786
A0A0H5SBJ0
E3MGD6
E3MGD5
//'''.encode("utf-8"))
return tmp_file.get_handle("r")
def patch_entrez_esearch(*args, **kwargs):
print("patch_entrez_esearch\nargs: %s\nkwargs: %s" % (args, kwargs))
if "rettype" in kwargs:
test_file = br.TempFile()
test_file.write("""<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD esearch 20060628//EN" \
"http://eutils.ncbi.nlm.nih.gov/eutils/dtd/20060628/esearch.dtd">
<eSearchResult>
<Count>5</Count>
</eSearchResult>
""")
handle = test_file.get_handle(mode="r")
else:
handle = open("%s/mock_resources/test_databasebuddy_clients/Entrez_esearch.xml" % hf.resource_path,
"r")
return handle
def test_liveshell_do_failures(monkeypatch, capsys):
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)
liveshell.do_failures("Blahh")
out, err = capsys.readouterr()
assert "No failures to report\n\n" in out
dbbuddy.failures["Foo"] = Db.Failure("Bar", "Fake failure")
liveshell.do_failures()
out, err = capsys.readouterr()
assert "The following failures have occured\n" in out
assert "Bar\nFake failure" in out
def test_liveshell_dump_session(monkeypatch):
monkeypatch.setattr(Db.LiveShell, "cmdloop", mock_cmdloop)
dbbuddy = Db.DbBuddy(_databases="uniprot")
dbbuddy.server_clients["uniprot"] = Db.UniProtRestClient(dbbuddy)
crash_file = br.TempFile(byte_mode=True)
liveshell = Db.LiveShell(dbbuddy, crash_file)
pre_dump = liveshell.crash_file.read()
liveshell.dump_session()
assert pre_dump == liveshell.crash_file.read()
liveshell.dbbuddy.search_terms.append("Blahh")
liveshell.dump_session()
assert pre_dump != liveshell.crash_file.read()
assert liveshell.dbbuddy.server_clients['uniprot'].lock
assert not liveshell.dbbuddy.server_clients['ensembl']
assert liveshell.undo
def test_liveshell_do_quit(monkeypatch, capsys):
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)
dbbuddy.records["Foo"] = "Bar"
monkeypatch.setattr(br, "ask", lambda _, **kwargs: False)
liveshell.do_quit(None)
out, err = capsys.readouterr()
assert "Aborted...\n\n" in out
with pytest.raises(SystemExit):
monkeypatch.setattr(br, "ask", lambda _, **kwargs: True)
liveshell.do_quit(None)
out, err = capsys.readouterr()
assert "Goodbye" in out
