def _run(self, atomspec):
# Execute "sample count" command for given atomspec
from chimerax.core.commands import run
from chimerax.core.logger import StringPlainTextLog
with StringPlainTextLog(self.session.logger) as log:
try:
run(self.session, "sample count " + atomspec)
finally:
html = "<pre>\n%s</pre>" % log.getvalue()
js = ('document.getElementById("output").innerHTML = %s'
% repr(html))
self.html_view.page().runJavaScript(js)
def f(session, batch_commands, q=q):
ret_dict = {}
for cmd in batch_commands:
with StringPlainTextLog(session.logger) as rest_log:
fname, args, kwargs = cmd
f_dict = ret_dict[fname] = {}
func = self.standard_functions.get(fname, None)
if func is None:
err_msg = 'Unrecognised function name: {}'.format(fname)
ret_dict['error'] = err_msg
break
f_dict.update(func(session, *args, **kwargs))
f_dict['log'] = rest_log.getvalue()
q.put(ret_dict)
def inner_func(session, *args, q=q, **kwargs):
from chimerax.core.logger import StringPlainTextLog
with StringPlainTextLog(session.logger) as rest_log:
ret = {}
try:
ret.update(func(session, *args, **kwargs))
except Exception as e:
import traceback
ret.update({
'error': str(e),
'traceback': traceback.format_exc()
})
ret['log'] = rest_log.getvalue()
q.put(ret)
def _run(path, logger, exit, unbound_method, *args, **kw):
from chimerax.core.logger import StringPlainTextLog
bb = _get_builder(path, logger)
exit_status = 0
if bb is not None:
with StringPlainTextLog(logger) as log:
try:
unbound_method(bb, *args, **kw)
except Exception:
import traceback
logger.bug(traceback.format_exc())
exit_status = 1
output = log.getvalue()
logger.info(output)
else:
exit_status = 1
if exit:
raise SystemExit(exit_status)
return exit_status
def f(args=args, session=session, q=q):
logger = session.logger
# rest_log.log_summary gets called at the end
# of the "with" statement
with StringPlainTextLog(logger) as rest_log:
from chimerax.core.commands import run
try:
commands = args["command"]
except KeyError:
logger.error("\"command\" parameter missing")
else:
try:
for cmd in commands:
if isinstance(cmd, bytes):
cmd = cmd.decode('utf-8')
run(session, cmd, log=False)
except NotABug as e:
logger.info(str(e))
q.put(rest_log.getvalue())