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_uniprotrestclient_query_uniprot(capsys, monkeypatch):
dbbuddy = Db.DbBuddy()
client = Db.UniProtRestClient(dbbuddy)
monkeypatch.setattr(Db, 'urlopen', mock_urlopen_handle_uniprot_ids)
client.query_uniprot("inx15", {"format": "list"})
assert client.results_file.read() == '''# Search: inx15
A8XEF9
O61786
A0A0H5SBJ0
//
'''
# Also make sure request_params can come in as a list
monkeypatch.setattr(Db, 'urlopen', mock_urlopen_handle_uniprot_ids)
client.query_uniprot("inx15", [{"format": "list"}])
# Errors
monkeypatch.setattr(Db, 'urlopen', mock_raise_httperror)
client.query_uniprot("inx15", [{"format": "list"}])
assert client.http_errors_file.read() == "Uniprot search failed for 'inx15'\nHTTP Error 101: " \
"Fake HTTPError from Mock\n//\n"
monkeypatch.setattr(Db, 'urlopen', mock_raise_urlerror_8)
client.query_uniprot("inx15", [{"format": "list"}])
assert "Uniprot request failed, are you connected to the internet?" in client.http_errors_file.read()
monkeypatch.setattr(Db, 'urlopen', mock_raise_urlerror)
client.query_uniprot("inx15", [{"format": "list"}])
assert "<urlopen error Fake URLError from Mock>" in client.http_errors_file.read()
params = {"format": "tab", "columns": "id,entry name,length,organism-id,organism,protein names,comments"}
client.query_uniprot("ABXEF9", params)
def test_uniprotrestclient_init():
dbbuddy = Db.DbBuddy(", ".join(ACCNS[3:6]))
client = Db.UniProtRestClient(dbbuddy)
assert hash(dbbuddy) == hash(client.dbbuddy)
assert client.server == 'http://www.uniprot.org/uniprot'
assert type(client.http_errors_file) == br.TempFile
assert type(client.results_file) == br.TempFile
assert client.max_url == 1000
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_uniprotrestclient_count_hits(monkeypatch):
dbbuddy = Db.DbBuddy("inx15,inx16")
client = Db.UniProtRestClient(dbbuddy)
monkeypatch.setattr(Db, 'urlopen', mock_urlopen_uniprot_count_hits)
assert client.count_hits() == 10
for indx in range(10):
client.dbbuddy.search_terms.append("a" * 110)
assert client.count_hits() == 20
monkeypatch.setattr(Db, 'urlopen', mock_raise_httperror)
assert client.count_hits() == 0
assert "d3b8e6bb4b9094117b7555b01dc85f64" in client.dbbuddy.failures
with pytest.raises(ValueError) as err:
client.dbbuddy.search_terms[0] = "a" * 1001
client.count_hits()
assert "Search term exceeds size limit of 1000 characters." in str(err)
def test_uniprotrestclient_fetch_proteins(monkeypatch, capsys, hf):
def patch_query_uniprot_search(*args, **kwargs):
print("patch_query_uniprot_search\nargs: %s\nkwargs: %s" %
(args, kwargs))
client.results_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)
//''', "w")
return
def patch_query_uniprot_fetch(*args, **kwargs):
print("patch_query_uniprot_fetch\nargs: %s\nkwargs: %s" %
(args, kwargs))
with open("%s/mock_resources/test_databasebuddy_clients/uniprot_fetch.txt" % hf.resource_path, "r") \
as ifile:
client.results_file.write(ifile.read(), "w")
return
def patch_query_uniprot_fetch_nothing(*args, **kwargs):
print("patch_query_uniprot_fetch_nothing\nargs: %s\nkwargs: %s" %
(args, kwargs))
client.results_file.write(
"# Search: A8XEF9,O61786,A0A0H5SBJ0,E3MGD6,O61787,A0A0V1AZ11,A8XEF8,A0A0B2VB60,"
"A0A0V0W5E2\n//\n//", "w")
return
monkeypatch.setattr(Db.UniProtRestClient, "query_uniprot", lambda _: True)
dbbuddy = Db.DbBuddy("inx15,inx16")
client = Db.UniProtRestClient(dbbuddy)
client.fetch_proteins()
out, err = capsys.readouterr()
assert client.results_file.read() == ""
assert "full records from UniProt..." not in err
# Test a single call to query_uniprot
monkeypatch.setattr(Db.UniProtRestClient, "query_uniprot",
patch_query_uniprot_search)
client.search_proteins()
monkeypatch.setattr(Db.UniProtRestClient, "query_uniprot",
patch_query_uniprot_fetch)
client.fetch_proteins()
out, err = capsys.readouterr()
assert "Requesting 9 full records from UniProt..." in err
# Test multicore call to query_uniprot
monkeypatch.setattr(br, "run_multicore_function",
patch_query_uniprot_fetch)
for accn, rec in client.dbbuddy.records.items():
rec.record = None
client.dbbuddy.records["a" * 999] = Db.Record("a" * 999,
_database="uniprot")
client.fetch_proteins()
out, err = capsys.readouterr()
assert "Requesting 10 full records from UniProt..." in err
seq = str(client.dbbuddy.records["A8XEF9"].record.seq)
assert hf.string2hash(seq) == "04f13629336cf6cdd5859c8913b742a5"
# Some edge cases
monkeypatch.setattr(Db.UniProtRestClient, "query_uniprot",
patch_query_uniprot_fetch_nothing)
client.http_errors_file.write("inx15\n%s\n//\n" %
URLError("Fake URLError from Mock"))
client.dbbuddy.records = OrderedDict([("a" * 999,
Db.Record("a" * 999,
_database="uniprot"))])
client.fetch_proteins()
out, err = capsys.readouterr()
assert "Requesting 1 full records from UniProt..." in err
assert "No sequences returned\n\n" in err
assert "The following errors were encountered while querying UniProt with fetch_proteins():" in err
assert hf.string2hash(str(
client.dbbuddy.records["a" *
999])) == "670bf9c6ae5832b42841798d882a7276"
with pytest.raises(ValueError) as err:
client.dbbuddy.records["a" * 1001] = Db.Record("a" * 1001,
_database="uniprot")
client.fetch_proteins()
assert "The provided accession or search term is too long (>1000)." in str(
err)
def test_uniprotrestclient_search_proteins(monkeypatch, capsys):
def patch_query_uniprot_multi(*args, **kwargs):
print("patch_query_uniprot_multi\nargs: %s\nkwargs: %s" %
(args, kwargs))
client1.results_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)
//''', "w")
return
def patch_query_uniprot_single(*args, **kwargs):
print("patch_query_uniprot_single\nargs: %s\nkwargs: %s" %
(args, kwargs))
client2.results_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
E3MGD6 E3MGD6_CAERE 384 31234 Caenorhabditis remanei (Caenorhabditis vulgaris) Innexin
//''', "w")
return
monkeypatch.setattr(Db.UniProtRestClient, "count_hits", lambda _: 0)
dbbuddy = Db.DbBuddy("inx15,inx16")
client1 = Db.UniProtRestClient(dbbuddy)
client1.search_proteins()
out, err = capsys.readouterr()
assert "Uniprot returned no results\n\n" in err
monkeypatch.setattr(Db.UniProtRestClient, "count_hits", lambda _: 9)
monkeypatch.setattr(br, "run_multicore_function",
patch_query_uniprot_multi)
client1.search_proteins()
out, err = capsys.readouterr()
assert "Retrieving summary data for 9 records from UniProt\n" in err
assert "Querying UniProt with 2 search terms (Ctrl+c to abort)\n" in err
assert len(dbbuddy.records) == 9
monkeypatch.setattr(Db.UniProtRestClient, "query_uniprot",
patch_query_uniprot_single)
dbbuddy = Db.DbBuddy("inx15")
client2 = Db.UniProtRestClient(dbbuddy)
client2.search_proteins()
out, err = capsys.readouterr()
assert "Querying UniProt with the search term 'inx15'...\n" in err
assert len(dbbuddy.records) == 4
