def _run_complexity_analysis(on_ci):
"""Generates cyclomatic complexity reports for the package
:param bool on_ci: Indicates whether an automated tool is running this operation. Output will be customized for
machine readability
"""
modlog.debug("Running complexity analysis")
# generate cyclomatic complexities for source files in XML format for integration with external tools
pyjen_path = os.path.join(os.getcwd(), "pyjen")
from radon.cli import cc
# TODO: output in XML format when running on CI
standard_output = StringIO()
with redirect_stdout(standard_output):
modlog.debug("Calling radon.cc")
cc(paths=[pyjen_path], show_complexity=True, show_closures=True, total_average=True, xml=on_ci)
modlog.debug("Writing report to disk")
cc_report = os.path.join(log_folder, "radon_complexity.xml")
with open(cc_report, "w") as fh:
fh.write(standard_output.getvalue())
standard_output.close()
modlog.info("Cyclomatic complexity analysis complete. See " + os.path.relpath(cc_report))
def test_simple_json_output():
output = StringIO()
reporter = JSONReporter()
linter = PyLinter(reporter=reporter)
checkers.initialize(linter)
linter.config.persistent = 0
linter.reporter.set_output(output)
linter.open()
linter.set_current_module("0123")
linter.add_message("line-too-long", line=1, args=(1, 2))
# we call this method because we didn't actually run the checkers
reporter.display_messages(None)
expected_result = [
[
("column", 0),
("line", 1),
("message", "Line too long (1/2)"),
("message-id", "C0301"),
("module", "0123"),
("obj", ""),
("path", "0123"),
("symbol", "line-too-long"),
("type", "convention"),
]
]
report_result = json.loads(output.getvalue())
report_result = [sorted(report_result[0].items(), key=lambda item: item[0])]
assert report_result == expected_result
def test_lazy_load_index():
f = StringIO()
dump({'wakka': 42}, f)
f.seek(0)
lj = LazyJSON(f)
assert_equal({'wakka': 10, '__total__': 0}, lj.offsets)
assert_equal({'wakka': 2, '__total__': 14}, lj.sizes)
def excerpt(mass, note_indices):
from patternfinder.geometric_helsinki.geometric_notes import NotePointSet
score = music21.converter.parse(PALESTRINA_PATH + mass + '.mid.xml')
pointset = list(NotePointSet(score).flat.notes)
pointset_indices = [int(i) for i in note_indices.split(',')]
score_note_ids = [pointset[i].original_note_id for i in pointset_indices]
# Get stream excerpt
_, start_measure = score.beatAndMeasureFromOffset(pointset[pointset_indices[0]].offset)
_, end_measure = score.beatAndMeasureFromOffset(pointset[pointset_indices[-1]].offset + pointset[-1].duration.quarterLength - 1)
excerpt = score.measures(numberStart=start_measure.number, numberEnd=end_measure.number)
# Colour notes
for note in excerpt.flat.notes:
if note.id in score_note_ids:
note.style.color = 'red'
# Delete part names (midi files have bad data)
for part in excerpt:
part.partName = ''
sx = music21.musicxml.m21ToXml.ScoreExporter(excerpt)
musicxml = sx.parse()
from io import StringIO
import sys
bfr = StringIO()
sys.stdout = bfr
sx.dump(musicxml)
output = bfr.getvalue()
sys.stdout = sys.__stdout__
return Response(output, mimetype='application/xml')
def stylesxml(self):
"""
Generates the styles.xml file
@return valid XML code as a unicode string
"""
xml=StringIO()
xml.write(_XMLPROLOGUE)
x = DocumentStyles()
x.write_open_tag(0, xml)
if self.fontfacedecls.hasChildNodes():
self.fontfacedecls.toXml(1, xml)
self.styles.toXml(1, xml)
a = AutomaticStyles()
a.write_open_tag(1, xml)
for s in self._used_auto_styles([self.masterstyles]):
s.toXml(2, xml)
a.write_close_tag(1, xml)
if self.masterstyles.hasChildNodes():
self.masterstyles.toXml(1, xml)
x.write_close_tag(0, xml)
result = xml.getvalue()
assert(type(result)==type(u""))
return result
def run(self):
try:
# Try parsing as XML
root = etree.parse(self.fn)
ns = "{%s}" % schemas['corpus']
out = StringIO()
for i in root.getiterator(ns + "entry"):
out.write(i.text + "\n")
self.corpus = out.getvalue()
del out
except:
# Turns out it's not XML
self.corpus = open(self.fn, 'r')
try:
open(self.dct) # test existence
except:
raise # TODO: wrap error for output
if not self.result:
delim = re.compile(r"\$[^^]*\^")
f = open(self.fn, 'r')
data = f.read()
f.close()
output = destxt(data).encode('utf-8')
timing_begin = time.time()
proc = Popen([self.app] + self.app_args + [self.dct], stdin=PIPE, stdout=PIPE, close_fds=True)
output = str(proc.communicate(output)[0].decode('utf-8'))
self.timer = time.time() - timing_begin
output = retxt(output)
output = delim.sub("$\n^", output)
self.result = output.split('\n')
return 0
def test_low_mapq(self):
""" We no longer fail reads because of low mapq.
When we use more than one reference, reads can receive low mapq if they
are in a conserved region that matches more than one reference.
"""
remap_file = StringIO("""\
qname,flag,rname,pos,mapq,cigar,rnext,pnext,tlen,seq,qual
Example_read_1,99,V3LOOP,1,44,32M,=,1,-32,TGTACAAGACCCAACAACAATACAAGAAAAAG,AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Example_read_1,147,V3LOOP,1,44,32M,=,1,-32,TGTACAAGACCCAACAACAATACAAGAAAAAG,AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Example_read_2,99,INT,1,8,32M,=,1,-32,TGTACAAGACCCAACAACAATACAAGAAAAAG,AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Example_read_2,147,INT,1,44,32M,=,1,-32,TGTACAAGACCCAACAACAATACAAGAAAAAG,AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
""")
expected_aligned_csv = """\
refname,qcut,rank,count,offset,seq
INT,15,0,1,0,TGTACAAGACCCAACAACAATACAAGAAAAAG
V3LOOP,15,0,1,0,TGTACAAGACCCAACAACAATACAAGAAAAAG
"""
expected_failed_csv = """\
qname,cause
"""
actual_aligned_csv = StringIO()
actual_failed_csv = StringIO()
sam2aln(remap_file,
actual_aligned_csv,
failed_csv=actual_failed_csv)
self.assertMultiLineEqual(expected_aligned_csv,
actual_aligned_csv.getvalue())
self.assertMultiLineEqual(expected_failed_csv,
actual_failed_csv.getvalue())
def _open(self):
header = StringIO(self.fp.read(24))
magic = header.read(4)
if magic != "FTEX":
raise ValueError("not a FTEX file")
version = unpack("i", header.read(4))
self.size = unpack("ii", header.read(8))
linesize = (self.size[0] + 3) / 4 * 8
mipmap_count, format_count = unpack("ii", header.read(8))
self.mode = "RGB"
self.tile = []
for i in range(format_count):
format, where = unpack("ii", self.fp.read(8))
if format == 0:
data = []
self.fp.seek(where)
size, = unpack("i", self.fp.read(4))
for yb in xrange((self.size[1] + 3) / 4):
decoded = dxtc.decodeDXT1(self.fp.read(linesize))
for d in decoded:
data.append(d)
data = "".join(data[:self.size[1]])
self.im = Image.core.new(self.mode, self.size)
return self.fromstring(data)
elif format == 1: # Uncompressed RGB
self.tile.append(("raw", (0, 0) + self.size, where+4, (self.mode, 0, 1)))
else:
raise ValueError("Invalid texture format (expected 0 or 1, got %i)" % (format))
def cmd(self, *args, **kw):
exit_code = kw.get('exit_code', 0)
fork = kw.get('fork', False)
if fork:
try:
output = subprocess.check_output((sys.executable, '-m', 'borg.archiver') + args)
ret = 0
except subprocess.CalledProcessError as e:
output = e.output
ret = e.returncode
output = os.fsdecode(output)
if ret != exit_code:
print(output)
self.assert_equal(exit_code, ret)
return output
args = list(args)
stdin, stdout, stderr = sys.stdin, sys.stdout, sys.stderr
try:
sys.stdin = StringIO()
output = StringIO()
sys.stdout = sys.stderr = output
ret = self.archiver.run(args)
sys.stdin, sys.stdout, sys.stderr = stdin, stdout, stderr
if ret != exit_code:
print(output.getvalue())
self.assert_equal(exit_code, ret)
return output.getvalue()
finally:
sys.stdin, sys.stdout, sys.stderr = stdin, stdout, stderr
def flush(self):
self.file.flush()
#super(TeeFile, self).flush()
StringIO.flush(self)
if self.queue is not None:
self.queue.put((current_process().pid, ''.join(self.queue_buffer)))
self.queue_buffer = []
def test_import_loop(self):
finders.get_finder.cache_clear()
err = StringIO()
with self.assertRaisesMessage(RuntimeError, 'Max post-process passes exceeded'):
call_command('collectstatic', interactive=False, verbosity=0, stderr=err)
self.assertEqual("Post-processing 'All' failed!\n\n", err.getvalue())
self.assertPostCondition()
def __repr__(self):
if self._parent is None:
return super().__repr__()
out = StringIO()
self.__call__(out=out)
return out.getvalue()
def call_command_returns(*args, **kwargs):
"call command but wich returns the output."
from django.core.management import call_command
stdout = StringIO()
kwargs['stdout'] = stdout
call_command(*args, **kwargs)
return stdout.getvalue().strip()
def scenario_parse_args_exits(self, argv):
with self.assertRaises(SystemExit) as cm:
stdout = StringIO()
stderr = StringIO()
with Redirect(stdout=stdout, stderr=stderr):
parsed_args = args.parse(argv)
return (stdout.getvalue(), stderr.getvalue(), cm.exception.code)
def export_set(dataset): """HTML representation of a Dataset.""" stream = StringIO() page = markup.page() page.table.open() if dataset.headers is not None: new_header = [item if item is not None else '' for item in dataset.headers] page.thead.open() headers = markup.oneliner.th(new_header) page.tr(headers) page.thead.close() for row in dataset: new_row = [item if item is not None else '' for item in row] html_row = markup.oneliner.td(new_row) page.tr(html_row) page.table.close() stream.writelines(str(page)) return stream.getvalue()
def results(id):
select_stmt = "SELECT q.name, d.name as department, q.description, q.query " \
"FROM query q JOIN departments d ON q.department_id = d.id " \
"WHERE q.id=%s;"
with RealDictConnection(dsn=local) as conn:
with conn.cursor() as cursor:
cursor.execute(select_stmt, (str(id), ))
res = cursor.fetchone()
if res:
with RealDictConnection(dsn=local) as conn:
with conn.cursor() as cursor:
cursor.execute(res['query'])
result = cursor.fetchall()
header = result[0].keys()
if request.args.get('download', '').strip():
si = StringIO()
f = csv.writer(si)
f.writerow(header)
f.writerows([row.values() for row in result])
output = make_response(si.getvalue())
output.headers["Content-Disposition"] = "attachment; filename=%s.csv" \
% str(res['name'])
output.headers["Content-type"] = "text/csv"
return output
else:
return render_template('results.html',
details=res, rows=result[0:5], id=id,
header=header)
else:
return 'Query with id %s does not exist!' % str(id)
def assertBlock(self, python, java):
self.maxDiff = None
dump = False
py_block = PyBlock(parent=PyModule('test', 'test.py'))
if python:
python = adjust(python)
code = compile(python, '<test>', 'exec')
py_block.extract(code, debug=dump)
java_code = py_block.transpile()
out = BytesIO()
constant_pool = ConstantPool()
java_code.resolve(constant_pool)
constant_pool.add(Utf8('test'))
constant_pool.add(Utf8('Code'))
constant_pool.add(Utf8('LineNumberTable'))
writer = ClassFileWriter(out, constant_pool)
java_code.write(writer)
debug = StringIO()
reader = ClassFileReader(BytesIO(out.getbuffer()), constant_pool, debug=debug)
JavaCode.read(reader, dump=0)
if dump:
print(debug.getvalue())
java = adjust(java)
self.assertEqual(debug.getvalue(), java[1:])
class DistantInteractiveConsole(InteractiveConsole):
def __init__(self, ipc):
InteractiveConsole.__init__(self, globals())
self.ipc = ipc
self.set_buffer()
def set_buffer(self):
self.out_buffer = StringIO()
sys.stdout = sys.stderr = self.out_buffer
def unset_buffer(self):
sys.stdout, sys.stderr = sys.__stdout__, sys.__stderr__
value = self.out_buffer.getvalue()
self.out_buffer.close()
return value
def raw_input(self, prompt=""):
output = self.unset_buffer()
# payload format: 'prompt' ? '\n' 'output'
self.ipc.send('\n'.join((prompt, output)))
cmd = self.ipc.recv()
self.set_buffer()
return cmd
def test_insertion(self):
remap_file = StringIO("""\
qname,flag,rname,pos,mapq,cigar,rnext,pnext,tlen,seq,qual
Example_read_1,99,V3LOOP,1,44,12M6I14M,=,1,-32,TGTACAAGACCCAACAACAATACAAGAAAAAG,AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Example_read_1,147,V3LOOP,1,44,12M6I14M,=,1,-32,TGTACAAGACCCAACAACAATACAAGAAAAAG,AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
""")
expected_aligned_csv = """\
refname,qcut,rank,count,offset,seq
V3LOOP,15,0,1,0,TGTACAAGACCCAATACAAGAAAAAG
"""
expected_insert_csv = """\
qname,fwd_rev,refname,pos,insert,qual
Example_read_1,F,V3LOOP,12,AACAAC,AAAAAA
Example_read_1,R,V3LOOP,12,AACAAC,AAAAAA
"""
actual_aligned_csv = StringIO()
actual_insert_csv = StringIO()
sam2aln(remap_file,
actual_aligned_csv,
actual_insert_csv)
self.assertMultiLineEqual(expected_aligned_csv,
actual_aligned_csv.getvalue())
self.assertMultiLineEqual(expected_insert_csv,
actual_insert_csv.getvalue())
class ContentState( State ):
""" This state records every line it meets as content until it reaches a line notifying a deposit reference or a publication reference.
Can return ``self`` or :class:`.PublicationState` or :class:`.DepositState`.
"""
def __init__( self, store ):
State.__init__( self, store )
self.textIO = StringIO()
def process_line( self, line ):
if publication_line_re.match( line ):
self.store_content()
return PublicationState( self.store ).process_line( line )
elif deposit_line_re.match( line ):
self.store_content()
return DepositState( self.store ).process_line( line )
else:
self.add_content_line( line )
globalOutputter.writeTagLine( 'TXT', line )
return self
def add_content_line( self, line ):
self.textIO.write( line )
self.textIO.write( '\n' )
def store_content( self ):
self.store['current_article']['content'] = self.textIO.getvalue()
def test_low_read_quality(self):
remap_file = StringIO("""\
qname,flag,rname,pos,mapq,cigar,rnext,pnext,tlen,seq,qual
Example_read_1,99,V3LOOP,1,44,32M,=,1,-32,TGTACAAGACCCAACAACAATACAAGAAAAAG,000000000000000000AAAAAAAAAAAAAA
Example_read_1,147,V3LOOP,1,44,32M,=,1,-32,TGTACAAGACCCAACAACAATACAAGAAAAAG,000000000000000000AAAAAAAAAAAAAA
Example_read_2,99,INT,1,44,32M,=,1,-32,TGTACAAGACCCAACAACAATACAAGAAAAAG,AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Example_read_2,147,INT,1,44,32M,=,1,-32,TGTACAAGACCCAACAACAATACAAGAAAAAG,AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
""")
expected_aligned_csv = """\
refname,qcut,rank,count,offset,seq
INT,15,0,1,0,TGTACAAGACCCAACAACAATACAAGAAAAAG
"""
expected_failed_csv = """\
qname,cause
Example_read_1,manyNs
"""
actual_aligned_csv = StringIO()
actual_failed_csv = StringIO()
sam2aln(remap_file,
actual_aligned_csv,
failed_csv=actual_failed_csv)
self.assertMultiLineEqual(expected_aligned_csv,
actual_aligned_csv.getvalue())
self.assertMultiLineEqual(expected_failed_csv,
actual_failed_csv.getvalue())
def test_opened_file(self):
sio = StringIO()
sio.write('test_data')
sio.seek(0)
file, close = open_if_filename(sio)
assert not close
eq_('test_data', file.read())
def contentxml(self):
"""
Generates the content.xml file
@return a bytestream in UTF-8 encoding
"""
xml=StringIO()
xml.write(_XMLPROLOGUE)
x = DocumentContent()
x.write_open_tag(0, xml)
if self.scripts.hasChildNodes():
self.scripts.toXml(1, xml)
if self.fontfacedecls.hasChildNodes():
self.fontfacedecls.toXml(1, xml)
a = AutomaticStyles()
stylelist = self._used_auto_styles([self.styles, self.automaticstyles, self.body])
if len(stylelist) > 0:
a.write_open_tag(1, xml)
for s in stylelist:
s.toXml(2, xml)
a.write_close_tag(1, xml)
else:
a.toXml(1, xml)
self.body.toXml(1, xml)
x.write_close_tag(0, xml)
return xml.getvalue().encode("utf-8")
def test_with_thumbor_disabled(self) -> None:
self.login(self.example_email("hamlet"))
fp = StringIO("zulip!")
fp.name = "zulip.jpeg"
result = self.client_post("/json/user_uploads", {'file': fp})
self.assert_json_success(result)
json = ujson.loads(result.content)
self.assertIn("uri", json)
uri = json["uri"]
base = '/user_uploads/'
self.assertEqual(base, uri[:len(base)])
quoted_uri = urllib.parse.quote(uri[1:], safe='')
with self.settings(THUMBOR_URL=''):
result = self.client_get("/thumbnail?url=%s&size=original" % (quoted_uri))
self.assertEqual(result.status_code, 302, result)
self.assertEqual(uri, result.url)
uri = 'https://www.google.com/images/srpr/logo4w.png'
quoted_uri = urllib.parse.quote(uri, safe='')
with self.settings(THUMBOR_URL=''):
result = self.client_get("/thumbnail?url=%s&size=original" % (quoted_uri))
self.assertEqual(result.status_code, 302, result)
self.assertEqual(uri, result.url)
uri = 'http://www.google.com/images/srpr/logo4w.png'
quoted_uri = urllib.parse.quote(uri, safe='')
with self.settings(THUMBOR_URL=''):
result = self.client_get("/thumbnail?url=%s&size=original" % (quoted_uri))
self.assertEqual(result.status_code, 302, result)
base = 'https://external-content.zulipcdn.net/7b6552b60c635e41e8f6daeb36d88afc4eabde79/687474703a2f2f7777772e676f6f676c652e636f6d2f696d616765732f737270722f6c6f676f34772e706e67'
self.assertEqual(base, result.url)
def testYAMLConfigFileParser_All(self):
try:
import yaml
except:
logging.warning("WARNING: PyYAML not installed. "
"Couldn't test YAMLConfigFileParser")
return
p = configargparse.YAMLConfigFileParser()
# test the all syntax case
config_lines = [
"a: '3'",
"list_arg:",
"- 1",
"- 2",
"- 3",
]
# test parse
input_config_str = StringIO("\n".join(config_lines)+"\n")
parsed_obj = p.parse(input_config_str)
# test serialize
output_config_str = p.serialize(parsed_obj)
self.assertEqual(input_config_str.getvalue(), output_config_str)
self.assertDictEqual(parsed_obj, dict([
('a', '3'),
('list_arg', [1,2,3]),
]))
def test_run_api_500_error():
os.environ["CODECLIMATE_API_HOST"] = "http://example.com"
api_mock = ApiMock()
api_mock.setup(500)
err = StringIO()
runner = Runner(["--file", "./coverage.txt", "--token", "token"], err=err)
orig_dir = os.getcwd()
os.chdir("./tests/fixtures")
subprocess.call(["git", "init"])
subprocess.call(["git", "config", "user.name", "Test User"])
subprocess.call(["git", "config", "user.email", "*****@*****.**"])
subprocess.call(["git", "commit", "--allow-empty", "--message", "init"])
try:
return_code = runner.run()
assert(return_code == 1)
assert("500 Server Error" in err.getvalue().strip())
finally:
del os.environ["CODECLIMATE_API_HOST"]
os.chdir(orig_dir)
shutil.rmtree("./tests/fixtures/.git")
api_mock.cleanup()
def get_tokens(self, text, unfiltered=False):
"""
Return an iterable of (tokentype, value) pairs generated from
`text`. If `unfiltered` is set to `True`, the filtering mechanism
is bypassed even if filters are defined.
Also preprocess the text, i.e. expand tabs and strip it if
wanted and applies registered filters.
"""
if isinstance(text, str):
if self.stripall:
text = text.strip()
elif self.stripnl:
text = text.strip('\n')
if sys.version_info[0] < 3 and isinstance(text, str):
text = StringIO(text.encode('utf-8'))
self.encoding = 'utf-8'
else:
text = StringIO(text)
def streamer():
for i, t, v in self.get_tokens_unprocessed(text):
yield t, v
stream = streamer()
if not unfiltered:
stream = apply_filters(stream, self.filters, self)
return stream
def correct_INCA_format(fp):
fp_list = list()
fp.seek(0)
if '(' in fp.readline():
for line in fp:
line = line.replace(
"(MLX::",
"").replace(
" : ",
"\t").replace(
" :",
"\t").replace(
" ",
"\t").lower().strip().replace(
")",
"\n")
if "record-by" in line:
if "image" in line:
line = "record-by\timage"
if "vector" in line:
line = "record-by\tvector"
if "dont-care" in line:
line = "record-by\tdont-care"
fp_list.append(line)
fp = StringIO()
fp.writelines(fp_list)
fp.seek(0)
return fp
def test_no_inherit_future(self):
# This file has from __future__ import print_function...
f = StringIO()
print('hello', file=f)
# ...but the template doesn't
exec_in('print >> f, "world"', dict(f=f))
self.assertEqual(f.getvalue(), 'hello\nworld\n')
def write_with_template(self, fname, tname, data):
fout = StringIO()
template = ezt.Template(compress_whitespace = 0)
template.parse_file(os.path.join('build', 'generator', tname))
template.generate(fout, data)
self.write_file_if_changed(fname, fout.getvalue())
