def test_ensembl_init(monkeypatch, hf):
def patch_ensembl_perform_rest_action(*args, **kwargs):
print("patch_ensembl_perform_rest_action\nargs: %s\nkwargs: %s" %
(args, kwargs))
test_files = "%s/mock_resources/test_databasebuddy_clients/" % hf.resource_path
if "info/species" in args:
with open("%s/ensembl_species.json" % test_files, "r") as ifile:
return json.load(ifile)
def patch_ensembl_perform_rest_action_empty(*args, **kwargs):
print("patch_ensembl_perform_rest_action\nargs: %s\nkwargs: %s" %
(args, kwargs))
return {}
monkeypatch.setattr(Db.EnsemblRestClient, "perform_rest_action",
patch_ensembl_perform_rest_action)
dbbuddy = Db.DbBuddy(", ".join(ACCNS[7:]))
client = Db.EnsemblRestClient(dbbuddy)
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 'vicugnapacos' in client.species['Alpaca']['aliases']
monkeypatch.setattr(Db.EnsemblRestClient, "perform_rest_action",
patch_ensembl_perform_rest_action_empty)
client = Db.EnsemblRestClient(dbbuddy)
assert client.species == {}
def test_ensembl_fetch_nucleotide(monkeypatch, capsys, hf):
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")
test_files = "%s/mock_resources/test_databasebuddy_clients/" % hf.resource_path
monkeypatch.setattr(Db.EnsemblRestClient, "perform_rest_action",
patch_ensembl_perform_rest_action)
dbbuddy = Db.DbBuddy(", ".join(ACCNS[7:]))
dbbuddy.records['ENSAMEG00000011912'] = Db.Record('ENSAMEG00000011912')
summary = OrderedDict([('organism', 'macropus_eugenii'),
('comments', 'Blahh blahh blahh'),
('name', 'Foo1')])
dbbuddy.records['ENSCJAG00000008732'].summary = summary
client = Db.EnsemblRestClient(dbbuddy)
client.fetch_nucleotide()
capsys.readouterr()
client.dbbuddy.print()
out, err = capsys.readouterr()
assert hf.string2hash(out + err) == "bc7610d5373db0b0fd9835410a182f10"
def test_ensembl_mc_search(monkeypatch, hf):
def patch_ensembl_perform_rest_action(*args, **kwargs):
print("patch_ensembl_perform_rest_action\nargs: %s\nkwargs: %s" %
(args, kwargs))
test_files = "%s/mock_resources/test_databasebuddy_clients/" % hf.resource_path
if "info/species" in args:
with open("%s/ensembl_species.json" % test_files, "r") as ifile:
return json.load(ifile)
elif "lookup/symbol/Mouse/Panx1" in args:
return json.loads(
'{"id": "ENSMUSG00000031934", "end": 15045478, "seq_region_name": "9", "description": '
'"pannexin 1 [Source:MGI Symbol;Acc:MGI:1860055]", "logic_name": "ensembl_havana_gene", '
'"species": "Mouse", "strand": -1, "start": 15005161, "db_type": "core", "assembly_name":'
' "GRCm38", "biotype": "protein_coding", "version": 13, "display_name": "Panx1", '
'"source": "ensembl_havana", "object_type": "Gene"}')
monkeypatch.setattr(Db.EnsemblRestClient, "perform_rest_action",
patch_ensembl_perform_rest_action)
dbbuddy = Db.DbBuddy(", ".join(ACCNS[7:]))
client = Db.EnsemblRestClient(dbbuddy)
client._mc_search('Mouse', ['Panx1'])
assert "'description': 'pannexin 1 [Source:MGI Symbol;Acc:MGI:1860055]'" in client.results_file.read(
)
monkeypatch.undo()
monkeypatch.setattr(Db, "Request", mock_raise_httperror)
client._mc_search('Mouse', ['Panx1'])
assert "HTTP Error 101: Fake HTTPError from Mock" in client.http_errors_file.read(
)
def test_search_ensembl(monkeypatch, capsys, hf):
def patch_ensembl_perform_rest_action(*args, **kwargs):
print("patch_ensembl_perform_rest_action\nargs: %s\nkwargs: %s" % (args, kwargs))
with open("%s/ensembl_species.json" % test_files, "r") as ifile:
return json.load(ifile)
def patch_search_ensembl_empty(*args, **kwargs):
print("patch_search_ensembl_empty\nargs: %s\nkwargs: %s" % (args, kwargs))
return
def patch_search_ensembl_results(*args, **kwargs):
print("patch_search_ensembl_empty\nargs: %s\nkwargs: %s" % (args, kwargs))
with open("%s/ensembl_search_results.txt" % test_files, "r") as ifile:
client.results_file.write(ifile.read())
return
test_files = "%s/mock_resources/test_databasebuddy_clients/" % hf.resource_path
monkeypatch.setattr(Db.EnsemblRestClient, "perform_rest_action", patch_ensembl_perform_rest_action)
monkeypatch.setattr(br, "run_multicore_function", patch_search_ensembl_empty)
dbbuddy = Db.DbBuddy(", ".join(ACCNS[7:]))
client = Db.EnsemblRestClient(dbbuddy)
client.dbbuddy.search_terms = ["Panx3"]
client.dbbuddy.records["ENSLAFG00000006034"] = Db.Record("ENSLAFG00000006034")
client.search_ensembl()
out, err = capsys.readouterr()
assert err == "Searching Ensembl for Panx3...\nEnsembl returned no results\n"
assert not client.dbbuddy.records["ENSLAFG00000006034"].record
monkeypatch.setattr(br, "run_multicore_function", patch_search_ensembl_results)
client.search_ensembl()
assert hf.string2hash(str(client.dbbuddy)) == "95dc1ecce077bef84cdf2d85ce154eef"
assert len(client.dbbuddy.records) == 44
assert client.dbbuddy.records["ENSLAFG00000006034"].database == "ensembl"
def test_ensembl_fetch_summaries(monkeypatch, capsys, hf):
def patch_species_fetch(*args, **kwargs):
print("patch_ensembl_perform_rest_action\nargs: %s\nkwargs: %s" %
(args, kwargs))
test_files = "%s/mock_resources/test_databasebuddy_clients/" % hf.resource_path
with open("%s/ensembl_species.json" % test_files, "r") as ifile:
return json.load(ifile)
def patch_ensembl_perform_rest_action_no_return(*args, **kwargs):
print("patch_ensembl_perform_rest_action\nargs: %s\nkwargs: %s" %
(args, kwargs))
return {}
def patch_ensembl_perform_rest_action(*args, **kwargs):
print("patch_ensembl_perform_rest_action\nargs: %s\nkwargs: %s" %
(args, kwargs))
return {
'ENSCJAG00000008732': {
'start': 49787361,
'logic_name': 'ensembl',
'display_name': 'Foo',
'seq_region_name': '7',
'version': 2,
'biotype': 'protein_coding',
'object_type': 'Gene',
'source': 'ensembl',
'end': 49814140,
'assembly_name': 'C_jacchus3.2.1',
'db_type': 'core',
'description': 'caspase 9 [Source:HGNC Symbol;Acc:HGNC:1511]',
'strand': -1,
'id': 'ENSCJAG00000008732'
},
'ENSAMEG00000011912': {}
}
monkeypatch.setattr(Db.EnsemblRestClient, "perform_rest_action",
patch_species_fetch)
dbbuddy = Db.DbBuddy(", ".join(ACCNS[7:]))
client = Db.EnsemblRestClient(dbbuddy)
monkeypatch.setattr(Db.EnsemblRestClient, "perform_rest_action",
patch_ensembl_perform_rest_action_no_return)
client.fetch_summaries()
capsys.readouterr()
client.dbbuddy.print()
out, err = capsys.readouterr()
assert hf.string2hash(out + err) == "8f251aee7d5efe536191b752e43f0d1a"
monkeypatch.setattr(Db.EnsemblRestClient, "perform_rest_action",
patch_ensembl_perform_rest_action)
client.fetch_summaries()
capsys.readouterr()
client.dbbuddy.print()
out, err = capsys.readouterr()
assert hf.string2hash(out + err) == "303bfe789a37c2a2263146e505d2147a"
assert client.dbbuddy.records['ENSCJAG00000008732'].summary[
'name'] == "Foo"
def test_ensembl_perform_rest_action(monkeypatch, hf):
def patch_ensembl_perform_rest_action(*args, **kwargs):
print("patch_ensembl_perform_rest_action\nargs: %s\nkwargs: %s" %
(args, kwargs))
test_files = "%s/mock_resources/test_databasebuddy_clients/" % hf.resource_path
with open("%s/ensembl_species.json" % test_files, "r") as ifile:
return json.load(ifile)
def patch_ensembl_urlopen(*args, **kwargs):
print("patch_ensembl_urlopen\nargs: %s\nkwargs: %s" % (args, kwargs))
outfile.clear()
if "lookup/symbol/Mouse/Panx1" in args[0].full_url:
outfile.write(
'{"id": "ENSMUSG00000031934", "end": 15045478, "seq_region_name": "9", "description": '
'"pannexin 1 [Source:MGI Symbol;Acc:MGI:1860055]", "logic_name": "ensembl_havana_gene", '
'"species": "Mouse", "strand": -1, "start": 15005161, "db_type": "core", "assembly_name":'
' "Foo", "biotype": "protein_coding", "version": 13, "display_name": "Panx1", '
'"source": "ensembl_havana", "object_type": "Gene"}'.encode())
elif "lookup/id" in args[0].full_url:
outfile.write(
'{"ENSPTRG00000014529":{"source":"ensembl","object_type":"Gene","logic_name":"ensembl",'
'"version":5,"species":"pan_troglodytes",'
'"description":"pannexin 2 [Source:VGNC Symbol;Acc:VGNC:5291]",'
'"display_name":"PANX_tuba!","assembly_name":"CHIMP2.1.4","biotype":"protein_coding",'
'"end":49082954,"seq_region_name":"22","db_type":"core","strand":1,'
'"id":"ENSPTRG00000014529","start":49073399}}'.encode())
elif "sequence/id" in args[0].full_url:
test_files = "%s/mock_resources/test_databasebuddy_clients/" % hf.resource_path
with open("%s/ensembl_sequence.seqxml" % test_files, "r") as ifile:
outfile.write(ifile.read().encode())
elif "error400" in args[0].full_url:
raise HTTPError(url="http://fake.come",
code=400,
msg="Bad request",
hdrs="Foo",
fp=StringIO("Bar"))
elif "error429" in args[0].full_url:
raise HTTPError(url="http://fake.come",
code=429,
msg="Server busy",
hdrs={'Retry-After': 0},
fp=StringIO("Bar"))
return outfile.get_handle("r")
outfile = br.TempFile(byte_mode=True)
monkeypatch.setattr(Db.EnsemblRestClient, "perform_rest_action",
patch_ensembl_perform_rest_action)
dbbuddy = Db.DbBuddy(", ".join(ACCNS[7:]))
client = Db.EnsemblRestClient(dbbuddy)
monkeypatch.undo() # Need to release perform_rest_action
monkeypatch.setattr(Db, "urlopen", patch_ensembl_urlopen)
# Search for gene identifiers and return summaries
data = client.perform_rest_action("lookup/symbol/Mouse/Panx1",
headers={
"Content-type": "application/json",
"Accept": "application/json"
})
assert data['assembly_name'] == 'Foo'
# Get summary from accn numbers
data = client.perform_rest_action("lookup/id",
data={"ids": ["ENSPTRG00000014529"]},
headers={
"Content-type": "application/json",
"Accept": "application/json"
})
assert data["ENSPTRG00000014529"]["display_name"] == "PANX_tuba!"
# Fetch sequence from accn numbers
data = client.perform_rest_action(
"sequence/id",
data={"ids": ["ENSPTRG00000014529"]},
headers={"Content-type": "text/x-seqxml+xml"})
assert hf.string2hash(
next(data).format("embl")) == "f4bb7d1ec812824b51f14d152e156f8f"
# Unrecognized endpoint header
with pytest.raises(ValueError) as err:
client.perform_rest_action("unknown/endpoint",
headers={"Content-type": "Foo/Bar"})
assert "Unknown request headers '{'Content-type': 'Foo/Bar'}'" in str(err)
# 400 error (with retry)
client.perform_rest_action("error400")
client.parse_error_file()
assert not client.dbbuddy.failures
# 429 error (with retry)
client.perform_rest_action("error429")
client.parse_error_file()
assert "39eaff4d057aa3d9d098be5cb50d2ce2" in client.dbbuddy.failures
# URLError
monkeypatch.setattr(Db, "urlopen", mock_raise_urlerror)
client.perform_rest_action("URLError")
client.parse_error_file()
assert 'eb498f0bcba3bfe69e4df6ee5bfbf6fb' in client.dbbuddy.failures
# URLError 8 (no internet)
monkeypatch.setattr(Db, "urlopen", mock_raise_urlerror_8)
client.perform_rest_action("URLError")
client.parse_error_file()
assert '57ad6fc317cf0d12ccb78d64d43682dc' in client.dbbuddy.failures
