def test_compile_dna_rvd_mix(self):
"""
Compile DNA and RVD mixture.
"""
text = pfusx.compile('NI NN NN NN HD NG NI NI NG NN NI NG NI NN NG',
'ATACCGTCTTATTTT')
json.loads(text)
def compile(text=None):
"""
Send provided code to the designated compiler and outputs a JSON
object detailing success or failure.
Success looks like:
{
"success": true,
"compiled_url": "http://example.com/rendered/foo.json",
"return_data": {"description":"A1: atcgtactgatc"}
}
Failure looks like:
{
"success": false,
"errors": ["First input should be different."]
}
Errors can be output to the user and vary by compiler. They're often
related to specific Mix.Bio form fields.
"""
text = request.args.get('input').strip().split('\n')
if not text:
return "handle_response(" + json.dumps({
'success': False,
'errors': ["No input provided."]
}) + ")"
# Compile the protocol, return any errors.
try:
protocol = pfusx.compile(*text)
except Exception as e:
return "handle_response(" + json.dumps({
'success': False,
'errors': [str(e)]
}) + ")"
description = json.loads(protocol)["info"]["description"]
# Save the data as a hash in the public dir where it can be downloaded.
content_hash = hashlib.sha224(protocol.encode('utf-8')).hexdigest()
fpath = os.path.dirname(os.path.realpath(__file__)) + "/static/protocols/"
fname = "ot_one_" + content_hash + ".json"
with open(fpath + fname, 'w') as f:
f.write(protocol)
output = {
"success": True,
"filename": 'https://api.mix.bio/static/protocols/' + fname,
"return_data": {
"description": description
}
}
return "handle_response(" + json.dumps(output) + ")"
def test_compile_dna_rvd_mix(self):
"""
Compile DNA and RVD mixture.
"""
text = pfusx.compile(
'NI NN NN NN HD NG NI NI NG NN NI NG NI NN NG',
'ATACCGTCTTATTTT'
)
json.loads(text)
def test_compile_invalid_sequence(self):
"""
Compiler validates input.
"""
with self.assertRaises(ValueError):
pfusx.compile("Cats with laser eyes.")
def test_compile_short_dna_input(self):
"""
Compiler should return error on short input.
"""
with self.assertRaises(ValueError):
pfusx.compile('GATTACA')
def test_compile_multi_dna(self):
"""
Should compile multiple DNA sequences.
"""
text = pfusx.compile('ATACCGTCTTATTTT', 'ATACCGTCTTATTTA')
json.loads(text)
def test_compile_dna(self):
"""
Should compile single DNA sequence.
"""
text = pfusx.compile('ATACCGTCTTATTTT')
json.loads(text)
def test_compile_invalid_sequence(self):
"""
Compiler validates input.
"""
with self.assertRaises(ValueError):
pfusx.compile("Cats with laser eyes.")
def test_compile_short_dna_input(self):
"""
Compiler should return error on short input.
"""
with self.assertRaises(ValueError):
pfusx.compile('GATTACA')
def test_compile_multi_dna(self):
"""
Should compile multiple DNA sequences.
"""
text = pfusx.compile('ATACCGTCTTATTTT', 'ATACCGTCTTATTTA')
json.loads(text)
def test_compile_dna(self):
"""
Should compile single DNA sequence.
"""
text = pfusx.compile('ATACCGTCTTATTTT')
json.loads(text)
