if inp_format == 'relaxedphyliptree':
invoc.extend(['-X', '-x'])
if idPrefix:
invoc.append('-t{u}'.format(u=idPrefix))
else:
invoc.append('-g')
for k, v in fa_dict.items():
if v > 0:
f = fa_flag[k]
invoc.append('-p{f}{v:d}'.format(f=f, v=v))
# Use new NCL option to emit only trees and taxa (not character data)
invoc.append('-etreenexml')
invoc.append('in.nex')
do_ext_proc_launch(request,
working_dir,
invoc,
NEXML_FILENAME,
ERR_FILENAME,
wait=block)
if not block:
time.sleep(timeout_duration)
status = invoc_status(request, working_dir)
assert (status != ExternalProcStatus.NOT_FOUND)
launched_this_call = True
if status == ExternalProcStatus.RUNNING:
if not launched_this_call:
time.sleep(timeout_duration)
status = invoc_status(request, working_dir)
if status == ExternalProcStatus.RUNNING:
return HTTP(102, "Process still running")
if status == ExternalProcStatus.FAILED:
try:
def to_nexml():
if len(request.args) == 1:
_LOG = get_logger(request, 'study')
try:
field = db['study_file']['file']
except Error:
sys.stderr.write('odd\n')
raise HTTP(404)
name = request.args[-1]
sys.stderr.write('looking for file "' + name + '"\n')
try:
ext_proc_dir = get_external_proc_dir_for_upload(request, db, name)
except ValueError:
raise HTTP(404)
if ext_proc_dir is None:
raise HTTP(404)
#@TEMPORARY could be refactored into a create_ext_proc_subdir() call
to_nexml_dir = os.path.join(ext_proc_dir, '2nexml')
if not os.path.exists(to_nexml_dir):
os.makedirs(to_nexml_dir)
_LOG.info('Created directory "%s"' % to_nexml_dir)
block = True
timeout_duration = 0.1 #@TEMPORARY should not be hard coded
out_filename = 'out.xml'
err_filename = 'err.txt'
#@TEMPORARY could be refactored into a launch_or_get_status() call
status = invoc_status(request, to_nexml_dir)
launched_this_call = False
if status == ExternalProcStatus.NOT_FOUND:
try:
try:
exe_path = get_conf(request).get("external", "2nexml")
except:
_LOG.warn("Config does not have external/2nexml setting")
raise
assert (os.path.exists(exe_path))
except:
_LOG.warn("Could not find the 2nexml executable")
raise HTTP(
501,
T("Server is not configured to allow 2nexml conversion"))
try:
(filename, upload_stream) = field.retrieve(name)
except IOError:
sys.stderr.write('not found\n')
raise HTTP(404)
do_ext_proc_launch(request,
to_nexml_dir, [exe_path, 'in.nex'],
out_filename,
err_filename, [('in.nex', upload_stream)],
wait=block)
if not block:
time.sleep(timeout_duration)
status = invoc_status(request, to_nexml_dir)
assert (status != ExternalProcStatus.NOT_FOUND)
launched_this_call = True
if status == ExternalProcStatus.RUNNING:
if not launched_this_call:
time.sleep(timeout_duration)
status = invoc_status(request, to_nexml_dir)
if status == ExternalProcStatus.RUNNING:
return HTTP(102, T("Process still running"))
#@TEMPORARY /end of potential launch_or_get_status call...
if status == ExternalProcStatus.FAILED:
try:
err_file = os.path.join(to_nexml_dir, err_filename)
err_content = 'Error message:\n ' + open(err_file, 'rU').read()
except:
err_content = ''
response.headers['Content-Type'] = 'text/xml'
raise HTTP(501, T("Conversion to NeXML failed.\n" + err_content))
output = os.path.join(to_nexml_dir, 'out.xml')
response.headers['Content-Type'] = 'text/xml'
return open(output, 'rU').read()
else:
raise HTTP(301)
return response.download(request, db)
def to_nexml():
if len(request.args) == 1:
_LOG = get_logger(request, 'study')
try:
field = db['study_file']['file']
except Error:
sys.stderr.write('odd\n')
raise HTTP(404)
name = request.args[-1]
sys.stderr.write('looking for file "' + name + '"\n')
try:
ext_proc_dir = get_external_proc_dir_for_upload(request, db, name)
except ValueError:
raise HTTP(404)
if ext_proc_dir is None:
raise HTTP(404)
#@TEMPORARY could be refactored into a create_ext_proc_subdir() call
to_nexml_dir = os.path.join(ext_proc_dir, '2nexml')
if not os.path.exists(to_nexml_dir):
os.makedirs(to_nexml_dir)
_LOG.info('Created directory "%s"' % to_nexml_dir)
block = True
timeout_duration = 0.1 #@TEMPORARY should not be hard coded
out_filename = 'out.xml'
err_filename = 'err.txt'
#@TEMPORARY could be refactored into a launch_or_get_status() call
status = invoc_status(request, to_nexml_dir)
launched_this_call = False
if status == ExternalProcStatus.NOT_FOUND:
try:
try:
exe_path = get_conf(request).get("external", "2nexml")
except:
_LOG.warn("Config does not have external/2nexml setting")
raise
assert(os.path.exists(exe_path))
except:
_LOG.warn("Could not find the 2nexml executable")
raise HTTP(501, T("Server is not configured to allow 2nexml conversion"))
try:
(filename, upload_stream) = field.retrieve(name)
except IOError:
sys.stderr.write('not found\n')
raise HTTP(404)
do_ext_proc_launch(request,
to_nexml_dir,
[exe_path, 'in.nex'],
out_filename,
err_filename,
[('in.nex', upload_stream)],
wait=block)
if not block:
time.sleep(timeout_duration)
status = invoc_status(request, to_nexml_dir)
assert(status != ExternalProcStatus.NOT_FOUND)
launched_this_call = True
if status == ExternalProcStatus.RUNNING:
if not launched_this_call:
time.sleep(timeout_duration)
status = invoc_status(request, to_nexml_dir)
if status == ExternalProcStatus.RUNNING:
return HTTP(102, T("Process still running"))
#@TEMPORARY /end of potential launch_or_get_status call...
if status == ExternalProcStatus.FAILED:
try:
err_file = os.path.join(to_nexml_dir, err_filename)
err_content = 'Error message:\n ' + open(err_file, 'rU').read()
except:
err_content = ''
response.headers['Content-Type'] = 'text/xml'
raise HTTP(501, T("Conversion to NeXML failed.\n" + err_content))
output = os.path.join(to_nexml_dir, 'out.xml')
response.headers['Content-Type'] = 'text/xml'
return open(output, 'rU').read()
else:
raise HTTP(301)
return response.download(request, db)
raise HTTP(501, T("Server is not configured to allow 2nexml conversion"))
invoc = [exe_path, '-f{f}'.format(f=inp_format), ]
if inp_format == 'relaxedphyliptree':
invoc.extend(['-X', '-x'])
if idPrefix:
invoc.append('-t{u}'.format(u=idPrefix))
else:
invoc.append('-g')
for k, v in fa_dict.items():
if v > 0:
f = fa_flag[k]
invoc.append('-p{f}{v:d}'.format(f=f, v=v))
invoc.append('in.nex')
do_ext_proc_launch(request,
working_dir,
invoc,
NEXML_FILENAME,
ERR_FILENAME,
wait=block)
if not block:
time.sleep(timeout_duration)
status = invoc_status(request, working_dir)
assert(status != ExternalProcStatus.NOT_FOUND)
launched_this_call = True
if status == ExternalProcStatus.RUNNING:
if not launched_this_call:
time.sleep(timeout_duration)
status = invoc_status(request, working_dir)
if status == ExternalProcStatus.RUNNING:
return HTTP(102, "Process still running")
if status == ExternalProcStatus.FAILED:
try:
