def back_translator():
"""
Back translator.
"""
output = Output(__file__)
output.addMessage(
__file__, -1, 'INFO',
'Received Back Translate request from {}'.format(request.remote_addr))
stats.increment_counter('back-translator/website')
description = request.args.get('description')
variants = []
if description:
variants = backtranslator.backtranslate(output, description)
errors, warnings, summary = output.Summary()
messages = map(util.message_info, output.getMessages())
output.addMessage(__file__, -1, 'INFO', 'Finished Back Translate request')
return render_template('back-translator.html',
errors=errors,
summary=summary,
description=description or '',
messages=messages,
variants=variants)
def test_np_no_nm(output):
"""
Back translate on NP without NM.
"""
variants = backtranslate(output, 'NP_000000.0:p.Asp92Tyr')
assert sorted(variants) == ['UNKNOWN:c.274G>T']
assert len(output.getMessagesWithErrorCode('WNOVERSION')) == 0
assert len(output.getMessagesWithErrorCode('WNODNA')) == 1
assert len(output.getMessagesWithErrorCode('WIMPROVE')) == 0
def test_nm_no_version(output):
"""
Back translate on NM.
"""
variants = backtranslate(output, 'NM_003002:p.Asp92Tyr')
assert sorted(variants) == ['NM_003002:c.274G>T']
assert len(output.getMessagesWithErrorCode('WNOVERSION')) == 0
assert len(output.getMessagesWithErrorCode('WNODNA')) == 0
assert len(output.getMessagesWithErrorCode('WIMPROVE')) == 0
def test_np_no_version(output):
"""
Back translate on NP.
"""
variants = backtranslate(output, 'NP_002993:p.Asp92Glu')
assert sorted(variants) == ['NM_003002:c.276C>A',
'NM_003002:c.276C>G']
assert len(output.getMessagesWithErrorCode('WNOVERSION')) == 1
assert len(output.getMessagesWithErrorCode('WNODNA')) == 0
assert len(output.getMessagesWithErrorCode('WIMPROVE')) == 0
def test_np_no_nm_improvable(output):
"""
Back translate on NP without NM improvable.
"""
variants = backtranslate(output, 'NP_000000.0:p.Leu92Phe')
assert sorted(variants) == ['UNKNOWN:c.274C>T',
'UNKNOWN:c.276A>C',
'UNKNOWN:c.276A>T',
'UNKNOWN:c.276G>C',
'UNKNOWN:c.276G>T']
assert len(output.getMessagesWithErrorCode('WNOVERSION')) == 0
assert len(output.getMessagesWithErrorCode('WNODNA')) == 1
assert len(output.getMessagesWithErrorCode('WIMPROVE')) == 1
def back_translator():
"""
Back translator.
"""
output = Output(__file__)
output.addMessage(
__file__, -1, 'INFO',
'Received Back Translate request from {}'.format(request.remote_addr))
stats.increment_counter('back-translator/website')
description = request.args.get('description')
variants = []
if description:
variants = backtranslator.backtranslate(output, description)
errors, warnings, summary = output.Summary()
messages = map(util.message_info, output.getMessages())
output.addMessage(__file__, -1, 'INFO', 'Finished Back Translate request')
return render_template(
'back-translator.html', errors=errors, summary=summary,
description=description or '', messages=messages, variants=variants)
