def get_structure(self, *args):
if len(args) == 2:
pdbId, fileName = args
elif len(args) == 1:
fileName = args[0]
pdbId, fileName = str(fileName), fileName
else:
raise ValueError(
"Error, input should be (id, fileName) or (fileName))")
if re.match("http(s?)://", fileName):
r = requests.get(fileName)
if r.ok:
fileName = StringIO(r.text)
else:
raise Exception("Error downloading pdb")
try:
if not isinstance(fileName, str) or not fileName.endswith(".gz"):
structure = PDBParser.get_structure(self, pdbId, fileName)
else:
with gzip.open(fileName) as f:
structure = PDBParser.get_structure(self, pdbId, f)
except Exception as e:
print(e)
structure = MMCIFParser.get_structure(self, pdbId, fileName)
if self.removeHeteroDuplicated:
structure = self.filterOutDuplicated(structure)
return structure
def __str__(self):
self.parse()
contents = StringIO()
for (line_type, components) in self._contents:
if line_type == 'blank':
contents.write("%s\n" % (components[0]))
elif line_type == 'all_comment':
contents.write("%s\n" % (components[0]))
elif line_type == 'hostname':
(hostname, tail) = components
contents.write("%s%s\n" % (hostname, tail))
# Ensure trailing newline
contents = contents.getvalue()
if not contents.endswith("\n"):
contents += "\n"
return contents
def __str__(self):
self.parse()
contents = StringIO()
for (line_type, components) in self._contents:
if line_type == 'blank':
contents.write("%s\n" % (components[0]))
elif line_type == 'all_comment':
contents.write("%s\n" % (components[0]))
elif line_type == 'hostname':
(hostname, tail) = components
contents.write("%s%s\n" % (hostname, tail))
# Ensure trailing newline
contents = contents.getvalue()
if not contents.endswith("\n"):
contents += "\n"
return contents
def test_from_python_output():
import logging, sys
if sys.version_info[0] < 3:
from StringIO import StringIO
else:
from io import StringIO
# create an artificial logger using the logging module
logger = logging.getLogger("XXX.YYY")
# add handlers
out, err = StringIO(), StringIO()
_warn_err = logging.StreamHandler(err)
_warn_err.setLevel(logging.WARNING)
logger.addHandler(_warn_err)
_debug_info = logging.StreamHandler(out)
_debug_info.setLevel(logging.DEBUG)
_debug_info.addFilter(bob.core.log._InfoFilter())
logger.addHandler(_debug_info)
# now, set up the logger
logger = bob.core.log.setup("XXX.YYY")
# send log messages
bob.core.log.set_verbosity_level(logger, 2)
logger.debug("This is a test debug message")
logger.info("This is a test info message")
bob.core.log.set_verbosity_level(logger, 0)
logger.warn("This is a test warn message")
logger.error("This is a test error message")
out = out.getvalue().rstrip()
err = err.getvalue().rstrip()
assert out.startswith("XXX.YYY")
assert "INFO" in out
assert out.endswith("This is a test info message")
assert err.startswith("XXX.YYY")
assert "ERROR" in err
assert err.endswith("This is a test error message")
def test_from_python_output():
import logging, sys
if sys.version_info[0] < 3:
from StringIO import StringIO
else:
from io import StringIO
# create an artificial logger using the logging module
logger = logging.getLogger("XXX.YYY")
# add handlers
out, err = StringIO(), StringIO()
_warn_err = logging.StreamHandler(err)
_warn_err.setLevel(logging.WARNING)
logger.addHandler(_warn_err)
_debug_info = logging.StreamHandler(out)
_debug_info.setLevel(logging.DEBUG)
_debug_info.addFilter(bob.extension.log._InfoFilter())
logger.addHandler(_debug_info)
# now, set up the logger
logger = bob.core.log.setup("XXX.YYY")
# send log messages
bob.core.log.set_verbosity_level(logger, 2)
logger.debug("This is a test debug message")
logger.info("This is a test info message")
bob.core.log.set_verbosity_level(logger, 0)
logger.warn("This is a test warn message")
logger.error("This is a test error message")
out = out.getvalue().rstrip()
err = err.getvalue().rstrip()
assert out.startswith("XXX.YYY")
assert "INFO" in out
assert out.endswith("This is a test info message")
assert err.startswith("XXX.YYY")
assert "ERROR" in err
assert err.endswith("This is a test error message")
def expand_macro(self, formatter, name, content):
(args, kwargs) = parse_args(content, False)
page_name = self.MACRO_PAGES + name
page = WikiPage(self.env, page_name)
if not page.exists:
raise RuntimeError(u'Can\'t find page', page_name)
for i, arg in enumerate(args):
kwargs[unicode(i+1)] = arg
text = RelaxedIdTemplate(page.text).safe_substitute(kwargs)
out = StringIO()
Formatter(self.env, formatter.context).format(text, out)
out = out.getvalue().strip()
if out.startswith(u'<p>'): out = out[3:]
if out.endswith(u'</p>'): out = out[:-4]
return out
