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')
if output == 'provenance':
PROV_FILEPATH = os.path.join(working_dir, PROV_FILENAME)
response.view = 'generic.json'
return json.load(codecs.open(PROV_FILEPATH, 'rU', encoding='utf-8'))
if output == 'input':
response.headers['Content-Type'] = 'text/plain'
return open(INPUT_FILEPATH, 'rU').read()
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')
if output == 'provenance':
PROV_FILEPATH = os.path.join(working_dir, PROV_FILENAME)
response.view = 'generic.json'
return json.load(codecs.open(PROV_FILEPATH, 'rU', encoding='utf-8'))
if output == 'input':
response.headers['Content-Type'] = 'text/plain'
return open(INPUT_FILEPATH, 'rU').read()
NEXML_FILEPATH = os.path.join(working_dir, NEXML_FILENAME)