def test_ncbiclient_fetch_sequences(hf, monkeypatch, capsys):
def patch_entrez_fetch_seq(*args, **kwargs):
print("patch_entrez_fetch_seq\nargs: %s\nkwargs: %s" % (args, kwargs))
test_file = "{0}mock_resources{1}test_databasebuddy_clients" \
"{1}Entrez_efetch_seq.gb".format(hf.resource_path, os.path.sep)
with open(test_file, "r") as ifile:
client.results_file.write(ifile.read())
# Empty DbBuddy
dbbuddy = Db.DbBuddy()
client = Db.NCBIClient(dbbuddy)
client.fetch_sequences("ncbi_prot")
assert hf.string2hash(str(dbbuddy)) == "016d020dd926f64ac1431f15c5683678"
# With records
monkeypatch.setattr(Db.NCBIClient, "_mc_query", patch_entrez_fetch_seq)
dbbuddy = Db.DbBuddy("XP_010103297.1,XP_010103298.1,XM_010104998.1")
client = Db.NCBIClient(dbbuddy)
client.fetch_sequences("ncbi_prot")
dbbuddy.out_format = "gb"
assert hf.string2hash(str(dbbuddy)) == "9bd8017da009696c1b6ebe5d4e3c0a89"
capsys.readouterr() # Clean up the buffer
dbbuddy.print()
out, err = capsys.readouterr()
out = re.sub(".*?sec.*?\n", "", out)
assert hf.string2hash(out) == "40b60e455df6ba092dbf96dc028ca82f"
def test_ncbiclient_fetch_summaries(hf, monkeypatch, capsys):
def patch_entrez_fetch_summaries(*args, **kwargs):
print("patch_entrez_fetch_summaries\nargs: %s\nkwargs: %s" % (args, kwargs))
if "esummary_seq" in kwargs["func_args"]:
test_file = "%s/mock_resources/test_databasebuddy_clients/Entrez_esummary_seq.xml" % hf.resource_path
with open(test_file, "r") as ifile:
client.results_file.write(ifile.read().strip())
client.results_file.write('\n### END ###\n')
elif "esummary_taxa" in kwargs["func_args"]:
test_file = "%s/mock_resources/test_databasebuddy_clients/Entrez_esummary_taxa.xml" % hf.resource_path
with open(test_file, "r") as ifile:
client.results_file.write(ifile.read().strip())
client.results_file.write('\n### END ###\n')
return
# No records to fetch
dbbuddy = Db.DbBuddy()
client = Db.NCBIClient(dbbuddy)
client.fetch_summaries("ncbi_prot")
assert not client.dbbuddy.records
monkeypatch.setattr(Db.NCBIClient, "_mc_query", patch_entrez_fetch_summaries)
dbbuddy = Db.DbBuddy("XP_010103297,XP_010103298.1,AAY72386.1")
client = Db.NCBIClient(dbbuddy)
capsys.readouterr()
client.fetch_summaries("ncbi_prot")
assert dbbuddy.records["AAY72386.1"].summary["organism"] == "Unclassified"
assert hf.string2hash(str(dbbuddy)) == "3a5e3379b12afe4044d2ece852ab2556"
def test_ncbiclient_search_ncbi(hf, monkeypatch, capsys):
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
monkeypatch.setattr(Db.Entrez, "esearch", patch_entrez_esearch)
monkeypatch.setattr(Db.NCBIClient, "fetch_summaries", lambda _: True)
monkeypatch.setattr(Db, "sleep", lambda _: True)
dbbuddy = Db.DbBuddy("XP_012618499.1")
client = Db.NCBIClient(dbbuddy)
dbbuddy.search_terms = []
client.search_ncbi("protein")
assert len(dbbuddy.records) == 1
dbbuddy.search_terms = ["casp9"]
client.search_ncbi("protein")
for accn in ["XP_012618499.1", "O88738.2", "O88879.3", "Q9NR09.2", "Q13075.3"]:
assert accn in dbbuddy.records
def test_ncbiclient_init():
dbbuddy = Db.DbBuddy(", ".join(ACCNS[:3]))
client = Db.NCBIClient(dbbuddy)
assert client.Entrez.email == br.config_values()['email']
assert client.Entrez.tool == "buddysuite"
assert hash(dbbuddy) == hash(client.dbbuddy)
assert type(client.http_errors_file) == br.TempFile
assert type(client.results_file) == br.TempFile
assert client.max_url == 1000
assert client.max_attempts == 5
def test_ncbiclient_fetch_summaries(hf, monkeypatch):
def patch_entrez_fetch_summaries(*args, **kwargs):
print("patch_entrez_fetch_summaries\nargs: %s\nkwargs: %s" %
(args, kwargs))
if kwargs["func_args"] == ["esummary_seq"]:
test_file = "%s/mock_resources/test_databasebuddy_clients/Entrez_esummary_seq.xml" % hf.resource_path
with open(test_file, "r") as ifile:
client.results_file.write(ifile.read().strip())
client.results_file.write('\n### END ###\n')
elif kwargs["func_args"] == ["esummary_taxa"]:
test_file = "%s/mock_resources/test_databasebuddy_clients/Entrez_esummary_taxa.xml" % hf.resource_path
with open(test_file, "r") as ifile:
client.results_file.write(ifile.read().strip())
client.results_file.write('\n### END ###\n')
elif kwargs["func_args"] == ["efetch_gi"]:
client.results_file.write("""703125407
703125412
67586143
### END ###
""")
return
# No records to fetch
dbbuddy = Db.DbBuddy()
client = Db.NCBIClient(dbbuddy)
client.fetch_summaries("ncbi_prot")
assert not client.dbbuddy.records
monkeypatch.setattr(Db.NCBIClient, "_mc_query",
patch_entrez_fetch_summaries)
dbbuddy = Db.DbBuddy("XP_010103297,XP_010103298.1,67586143,257467473")
client = Db.NCBIClient(dbbuddy)
client.fetch_summaries("ncbi_prot")
for accn, rec in dbbuddy.records.items():
assert rec.gi in [703125407, 703125412, 67586143, 257467473]
assert dbbuddy.records["AAY72386.1"].summary["organism"] == "Unclassified"
assert hf.string2hash(str(dbbuddy)) == "0cf7c9ccf058cf3b50d2aab7ecb1f953"
def test_ncbiclient_search_ncbi(hf, monkeypatch, capsys):
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
monkeypatch.setattr(Db.Entrez, "esearch", patch_entrez_esearch)
monkeypatch.setattr(Db.NCBIClient, "fetch_summaries", lambda _: True)
monkeypatch.setattr(Db, "sleep", lambda _: True)
dbbuddy = Db.DbBuddy("909549231")
client = Db.NCBIClient(dbbuddy)
dbbuddy.search_terms = []
client.search_ncbi("protein")
assert len(dbbuddy.records) == 1
dbbuddy.search_terms = ["casp9"]
client.search_ncbi("protein")
for accn in [
"909549231", "909549227", "909549224", "909546647", "306819620"
]:
assert accn in dbbuddy.records
monkeypatch.setattr(Db.Entrez, "esearch", mock_raise_keyboardinterrupt)
client.search_ncbi("protein")
out, err = capsys.readouterr()
assert 'NCBI returned no protein results' in err
def test_ncbiclient_mc_query(hf, monkeypatch):
def patch_entrez_esummary_taxa(*args, **kwargs):
print("patch_entrez_esummary_taxa\nargs: %s\nkwargs: %s" %
(args, kwargs))
test_file = "%s/mock_resources/test_databasebuddy_clients/Entrez_esummary_taxa.xml" % hf.resource_path
return open(test_file, "r")
def patch_entrez_efetch_gis(*args, **kwargs):
print("patch_entrez_efetch_gis\nargs: %s\nkwargs: %s" % (args, kwargs))
tmp_file = br.TempFile()
tmp_file.write("703125407\n703125412\n67586143\n")
return tmp_file.get_handle("r")
def patch_entrez_esummary_seq(*args, **kwargs):
print("patch_entrez_esummary_seq\nargs: %s\nkwargs: %s" %
(args, kwargs))
test_file = "%s/mock_resources/test_databasebuddy_clients/Entrez_esummary_seq.xml" % hf.resource_path
return open(test_file, "r")
def patch_entrez_efetch_seq(*args, **kwargs):
print("patch_entrez_efetch_seq\nargs: %s\nkwargs: %s" % (args, kwargs))
test_file = "%s/mock_resources/test_databasebuddy_clients/Entrez_efetch_seq.gb" % hf.resource_path
return open(test_file, "r")
monkeypatch.setattr(Db, "sleep",
lambda _: True) # No need to wait around for stuff...
dbbuddy = Db.DbBuddy()
client = Db.NCBIClient(dbbuddy)
monkeypatch.setattr(Db.Entrez, "esummary", patch_entrez_esummary_taxa)
client._mc_query("649,734,1009,2302", ["esummary_taxa"])
assert hf.string2hash(
client.results_file.read()) == "acfb85bbdf7c2f8ea7e925c5bfcaaf06"
client.results_file.clear()
monkeypatch.setattr(Db.Entrez, "efetch", patch_entrez_efetch_gis)
client._mc_query("XP_010103297.1,XP_010103298.1,XP_010103299.1",
["efetch_gi"])
assert client.results_file.read(
) == "703125407\n703125412\n67586143\n### END ###\n"
client.results_file.clear()
monkeypatch.setattr(Db.Entrez, "esummary", patch_entrez_esummary_seq)
client._mc_query("703125407,703125412,67586143", ["esummary_seq"])
assert hf.string2hash(
client.results_file.read()) == "e6ba80b5fe2f35002ac2227ca7791c17"
client.results_file.clear()
monkeypatch.setattr(Db.Entrez, "efetch", patch_entrez_efetch_seq)
client._mc_query("703125407,703125412,67586143", ["efetch_seq"])
assert hf.string2hash(
client.results_file.read()) == "0154d7bd9d47ca6abac00f25428b9e7e"
monkeypatch.undo()
monkeypatch.setattr(Db, "sleep", lambda _: True)
with pytest.raises(ValueError) as err:
client._mc_query("703125407", ["foo"])
assert "'tool' argument must be in 'esummary_taxa', 'efetch_gi', 'esummary_seq', or 'efetch_seq'" in str(
err)
with pytest.raises(ValueError) as err:
client._mc_query("703125407", ["foo", "Bar"])
assert "Unknown type 'Bar', choose between 'nucleotide' and 'protein" in str(
err)
monkeypatch.setattr(Db.Entrez, "efetch", mock_raise_httperror)
client._mc_query("703125407,703125412,67586143", ["efetch_seq"])
assert "NCBI request failed: 703125407,703125412,67586143\nHTTP Error 101: Fake HTTPError from Mock\n//" \
in client.http_errors_file.read()
assert "Service unavailable" not in client.http_errors_file.read()
monkeypatch.setattr(Db.Entrez, "efetch", mock_raise_503_httperror)
client._mc_query("703125407", ["efetch_seq"])
assert "Service unavailable" in client.http_errors_file.read()
monkeypatch.setattr(Db.Entrez, "efetch", mock_raise_connectionreseterror)
client._mc_query("703125407", ["efetch_seq"])
assert "NCBI request failed: 703125407\nFake ConnectionResetError from Mock: [Errno 54] Connection reset by peer"\
in client.http_errors_file.read()
assert "are you connected to the internet?" not in client.http_errors_file.read(
)
monkeypatch.setattr(Db.Entrez, "efetch", mock_raise_urlerror_8)
client._mc_query("703125407", ["efetch_seq"])
assert "are you connected to the internet?" in client.http_errors_file.read(
)
assert "<urlopen error Fake URLError from Mock>" not in client.http_errors_file.read(
)
monkeypatch.setattr(Db.Entrez, "efetch", mock_raise_urlerror)
client._mc_query("703125407", ["efetch_seq"])
assert "<urlopen error Fake URLError from Mock>" in client.http_errors_file.read(
)
