if not os.path.exists(NEXSON_DONE_FILEPATH):
dfj = get_ot_study_info_from_nexml(NEXML_FILEPATH,
nexson_syntax_version=NEXSON_VERSION)
out = codecs.open(NEXSON_FILEPATH, 'w', encoding='utf-8')
json.dump(dfj, out, indent=0, sort_keys=True)
out.write('\n')
out.close()
out = open(NEXSON_DONE_FILEPATH, 'w')
out.write('0\n')
out.close()
except locket.LockError:
return HTTP(102, "Conversion to NexSON still running")
if output in ['nexson', 'ot:nexson']:
response.view = 'generic.json'
nex = json.load(codecs.open(NEXSON_FILEPATH, 'rU', encoding='utf-8'))
num_trees = count_num_trees(nex, NEXSON_VERSION)
r = {'data': nex}
bundle_properties = json.load(codecs.open(RETURN_ATT_FILEPATH, 'rU', encoding='utf-8'))
try:
dd = bundle_properties.get('dataDeposit')
if dd:
n = nex.get('nex:nexml') or nex['nex']
add_resource_meta(n, "ot:dataDeposit", dd, NEXSON_VERSION)
except:
pass
r.update(bundle_properties)
r['numberOfTrees'] = num_trees
r['nexml2json'] = NEXSON_VERSION
read_inp_format = bundle_properties.get('inputFormat', '')
read_filename = bundle_properties.get('filename', '')
400,
T("Submitted data is not a valid NeXML file, or cannot be converted."
))
out = codecs.open(NEXSON_FILEPATH, 'w', encoding='utf-8')
json.dump(dfj, out, indent=0, sort_keys=True)
out.write('\n')
out.close()
out = open(NEXSON_DONE_FILEPATH, 'w')
out.write('0\n')
out.close()
except locket.LockError:
return HTTP(102, "Conversion to NexSON still running")
if output in ['nexson', 'ot:nexson']:
response.view = 'generic.json'
nex = json.load(codecs.open(NEXSON_FILEPATH, 'rU', encoding='utf-8'))
num_trees = count_num_trees(nex, NEXSON_VERSION)
r = {'data': nex}
bundle_properties = json.load(
codecs.open(RETURN_ATT_FILEPATH, 'rU', encoding='utf-8'))
try:
dd = bundle_properties.get('dataDeposit')
if dd:
n = nex.get('nex:nexml') or nex['nex']
add_resource_meta(n, "ot:dataDeposit", dd, NEXSON_VERSION)
except:
pass
r.update(bundle_properties)
r['numberOfTrees'] = num_trees
r['nexml2json'] = NEXSON_VERSION
read_inp_format = bundle_properties.get('inputFormat', '')
read_filename = bundle_properties.get('filename', '')
def testCanCountTrees(self):
for v in ['0.0', '1.0', '1.2']:
inp = pathmap.nexson_obj('otu/v{v}.json'.format(v=v))
self.assertEqual(1, count_num_trees(inp, v))
