elif request.vars.content is not None:
upload_stream = request.vars.content # stream is a bad name, but write_input_files does the write thing.
file_extensions = {
'nexson': '.json',
'nexus': '.nex',
'nexml': '.nexml',
'newick': '.tre',
'relaxedphyliptree': '.tre'
}
filename = 'PASTED%s' % (file_extensions.get(inp_format), )
else:
raise HTTP(
400,
'Expecting a "file" argument with an input file or a "content" argument with the contents of in input file'
)
write_input_files(request, working_dir,
[(INPUT_FILENAME, upload_stream)])
prov_info = {
'filename': filename,
'dateTranslated': datetime.datetime.utcnow().isoformat(),
}
if request.vars.dataDeposit:
prov_info['dataDeposit'] = request.vars.dataDeposit
write_ext_proc_content(
request,
working_dir, [(PROV_FILENAME, json.dumps(prov_info))],
encoding='utf-8')
orig_args.update(prov_info)
write_ext_proc_content(
request,
working_dir,
[(RETURN_ATT_FILENAME, json.dumps(orig_args))],
inpfp = os.path.join(working_dir, INPUT_FILENAME)
if is_upload:
with locket.lock_file(INP_LOCKFILEPATH):
if not os.path.exists(INPUT_FILEPATH):
if request.vars.file is not None:
upf = request.vars.file
upload_stream = upf.file
filename = upf.filename
elif request.vars.content is not None:
upload_stream = request.vars.content # stream is a bad name, but write_input_files does the write thing.
file_extensions = {'nexson':'.json', 'nexus':'.nex', 'nexml':'.nexml', 'newick':'.tre', 'relaxedphyliptree':'.tre'}
filename = 'PASTED%s' % (file_extensions.get(inp_format),)
else:
raise HTTP(400, 'Expecting a "file" argument with an input file or a "content" argument with the contents of in input file')
write_input_files(request, working_dir, [(INPUT_FILENAME, upload_stream)])
prov_info = {
'filename' : filename,
'dateTranslated': datetime.datetime.utcnow().isoformat(),
}
if request.vars.dataDeposit:
prov_info['dataDeposit'] = request.vars.dataDeposit
write_ext_proc_content(request,
working_dir,
[(PROV_FILENAME, json.dumps(prov_info))],
encoding='utf-8')
orig_args.update(prov_info)
write_ext_proc_content(request,
working_dir,
[(RETURN_ATT_FILENAME, json.dumps(orig_args))],
encoding='utf-8')