def quote_newick_name(s, needs_quotes_pattern=_NEWICK_NEEDING_QUOTING):
s = UNICODE(s)
if "'" in s:
return u"'{}'".format("''".join(s.split("'")))
if needs_quotes_pattern.search(s):
return u"'{}'".format(s)
return s
def _process_query_dict(self, query_dict, valid_keys, kwargs):
if query_dict is None:
query_dict = {}
for k, v in kwargs.items():
if k in valid_keys:
query_dict[k] = v
else:
query_dict['ot:' + k] = v
nq = len(query_dict)
if nq == 0:
if self.use_v1:
raise ValueError(
'The property/value pairs for the query should be passed in as keyword arguments'
)
return None
if nq > 1:
raise NotImplementedError(
'Currently only searches for one property/value pair are supported'
)
k = list(query_dict.keys())[0]
if k not in valid_keys:
m = '"{k}" is not a valid search term. Expecting it to be one of the following: {kl}'
m = m.format(k=k, kl=repr(valid_keys))
raise ValueError(m)
v = query_dict[k]
if not is_str_type(v):
v = UNICODE(v)
if k == 'ot:studyPublication':
v = doi2url(v)
return (k, v)
def _dict_summary(d, name):
dk = list(d.keys())
dk.sort()
sd = UNICODE(d)
if len(sd) < _CUTOFF_LEN_DETAILED_VIEW:
a = []
for k in dk:
a.extend([repr(k), ': ', repr(d[k]), ', '])
return u'%s={%s}' % (name, ''.join(a))
return u'%s-keys=%s' % (name, repr(dk))
def testValidFilesPass(self):
# just one test file for now
msg = ''
frag = 'amendment-good.json'
amendment = pathmap.amendment_obj(frag)
aa = validate_amendment(amendment)
errors = aa[0]
for e in errors:
_LOG.debug('unexpected error from {f}: {m}'.format(f=frag, m=UNICODE(e)))
if len(errors) > 0:
ofn = pathmap.amendment_source_path(frag + '.output')
testing_write_json(errors, ofn)
msg = "File failed to validate cleanly. See {o}".format(o=ofn)
self.assertEqual(len(errors), 0, msg)
def testValidFilesPass(self):
format_list = ['1.2']
msg = ''
for d in VALID_NEXSON_DIRS:
for nf in format_list:
frag = os.path.join(d, 'v{f}.json'.format(f=nf))
nexson = pathmap.nexson_obj(frag)
aa = validate_nexson(nexson)
annot = aa[0]
for e in annot.errors:
_LOG.debug('unexpected error from {f}: {m}'.format(
f=frag, m=UNICODE(e)))
if len(annot.errors) > 0:
ofn = pathmap.nexson_source_path(frag + '.output')
ew_dict = annot.get_err_warn_summary_dict()
testing_write_json(ew_dict, ofn)
msg = "File failed to validate cleanly. See {o}".format(
o=ofn)
self.assertEqual(len(annot.errors), 0, msg)
def _partition_keys_for_xml(self, o):
'''Breaks o into four content type by key syntax:
attrib keys (start with '@'),
text (value associated with the '$' or None),
child element keys (all others)
meta element
'''
ak = {}
tk = None
ck = {}
mc = {}
#_LOG.debug('o = {o}'.format(o=o))
for k, v in o.items():
if k.startswith('@'):
if k == '@xmlns':
if '$' in v:
ak['xmlns'] = v['$']
for nsk, nsv in v.items():
if nsk != '$':
ak['xmlns:' + nsk] = nsv
else:
s = k[1:]
if type(v) == bool:
if v == True:
v = u'true'
else:
v = u'false'
ak[s] = UNICODE(v)
elif k == '$':
tk = v
elif k.startswith('^') and (not self._migrating_from_bf):
s = k[1:]
val = _convert_hbf_meta_val_for_xml(s, v)
_add_value_to_dict_bf(mc, s, val)
elif (k == u'meta') and self._migrating_from_bf:
s, val = _convert_bf_meta_val_for_xml(v)
_add_value_to_dict_bf(mc, s, val)
else:
ck[k] = v
return ak, tk, ck, mc
def _create_sub_el(doc, parent, tag, attrib, data=None):
'''Creates and xml element for the `doc` with the given `parent`
and `tag` as the tagName.
`attrib` should be a dictionary of string keys to primitives or dicts
if the value is a dict, then the keys of the dict are joined with
the `attrib` key using a colon. This deals with the badgerfish
convention of nesting xmlns: attributes in a @xmnls object
If `data` is not None, then it will be written as data. If it is a boolean,
the xml true false will be writtten. Otherwise it will be
converted to python unicode string, stripped and written.
Returns the element created
'''
el = doc.createElement(tag)
if attrib:
if ('id' in attrib) and ('about' not in attrib):
about_val = '#' + attrib['id']
el.setAttribute('about', about_val)
for att_key, att_value in attrib.items():
if isinstance(att_value, dict):
for inner_key, inner_val in att_value.items():
rk = ':'.join([att_key, inner_key])
el.setAttribute(rk, inner_val)
else:
el.setAttribute(att_key, att_value)
if parent:
parent.appendChild(el)
if data:
if data is True:
el.appendChild(doc.createTextNode('true'))
elif data is False:
el.appendChild(doc.createTextNode('false'))
else:
u = UNICODE(data).strip()
if u:
el.appendChild(doc.createTextNode(u))
return el