def multipartite_view_add(request):
context = RequestContext(request)
context.update(csrf(request))
request_data = request.POST
if not request_data:
return render_to_response('goldenbraid_info.html',
{'info': "Not enougth data to add the feature"},
context_instance=RequestContext(request))
multi_type = request_data['category']
allowed_categories = PARTS_TO_ASSEMBLE.keys() + ['free']
if multi_type is None or multi_type not in allowed_categories:
return render_to_response('goldenbraid_info.html',
{'info': "Not enougth data to add the feature"},
context_instance=RequestContext(request))
if multi_type == 'free':
part_types = request_data['order'].split(':')
else:
part_types = [p[0] for p in PARTS_TO_ASSEMBLE[multi_type]]
multi_data = {'Vector': request_data['Vector']}
for part_type in part_types:
multi_data[part_type] = request_data[part_type]
assembled_seq = assemble_parts(multi_data, part_types)
name = request_data['name']
temp_fhand = NamedTemporaryFile(prefix='{0}.'.format(assembled_seq.id),
suffix='.gb')
temp_fhand.write(assembled_seq.format('gb'))
temp_fhand.flush()
temp_fhand.seek(0)
props = {'Description': [request_data['description']],
'Reference': [request_data['reference']]}
try:
feature = add_feature(name=name, type_name=TU_TYPE_NAME,
vector=request_data['Vector'],
genbank=temp_fhand, props=props,
owner=request.user, is_public=False)
except IntegrityError as error:
print error
if 'feature already in db' in str(error):
# TODO choose a template
return render_to_response('feature_exists.html',
{},
context_instance=RequestContext(request))
else:
return HttpResponseServerError()
except Exception as error:
print error
return HttpResponseServerError()
# if everithing os fine we show the just added feature
return redirect(feature.url)
def test_add_feature(self):
'It tests the add_feature function'
name = 'test_name'
type_name = VECTOR_TYPE_NAME
vector = None
genbank = os.path.join(TEST_DATA, 'pANT1_uniq.gb')
props = {ENZYME_IN_TYPE_NAME: ['BsaI'],
ENZYME_OUT_TYPE_NAME: ['BsaI']}
try:
add_feature(name, type_name, vector, open(genbank), props,
'test_user')
self.fail()
except RuntimeError as error:
if 'the given user does not exist' in str(error):
pass
else:
raise
User.objects.create_user(username='******', email='*****@*****.**',
password='******')
add_feature(name, type_name, vector, open(genbank), props, 'admin')
feat = Feature.objects.get(uniquename='pANT1_uniq')
assert FeatureRelationship.objects.filter(object=feat).count() == 0
assert feat.uniquename == "pANT1_uniq"
os.remove(os.path.join(proj_settings.MEDIA_ROOT,
feat.genbank_file.name))
# add relationships to feature
# first we need to add derives from to db as it is not in the fixtures
name = 'GB_UA_17A'
vector = 'pDGB1_alpha1'
type_name = TU_TYPE_NAME
genbank = os.path.join(TEST_DATA, 'GB_UA_17A.gb')
props = {ENZYME_IN_TYPE_NAME: ['BsaI'],
ENZYME_OUT_TYPE_NAME: ['BsaI']}
# add_feature(name, type_name, vector, open(genbank), props, 'admin')
feat = Feature.objects.get(uniquename='GB_UA_17A')
assert FeatureRelationship.objects.filter(object=feat).count() == 2
def crispr_view_add(request):
context = RequestContext(request)
context.update(csrf(request))
request_data = request.POST
# request_data
seq = request_data['seq']
category = request_data['category']
prefix = request_data['prefix']
suffix = request_data['suffix']
seq_name = request_data['seq_name']
name = request_data['name']
if category == 'None':
category_name = 'Other'
else:
category_name = CRYSPER_CATEGORIES[category][0]
print 'seq', seq
seq = SeqRecord(Seq(seq, DNAAlphabet()), id=seq_name, name=seq_name)
print 'seq', seq
temp_fhand = NamedTemporaryFile(prefix='{0}.'.format(seq.id),
suffix='.gb')
temp_fhand.write(seq.format('gb'))
temp_fhand.flush()
temp_fhand.seek(0)
props = {'Description': [request_data['description']],
'Reference': [request_data['reference']]}
try:
feature = add_feature(name=name, type_name=category_name,
vector=None, genbank=temp_fhand, props=props,
owner=request.user, is_public=False,
prefix=prefix, suffix=suffix)
except IntegrityError as error:
print error
if 'feature already in db' in str(error):
# TODO choose a template
return render_to_response('feature_exists.html',
{},
context_instance=RequestContext(request))
else:
return HttpResponseServerError()
except Exception as error:
raise
print error
return HttpResponseServerError(error)
# if everithing os fine we show the just added feature
return redirect(feature.url)
def bipartite_view_add(request):
context = RequestContext(request)
context.update(csrf(request))
request_data = request.POST
if not request_data:
return render_to_response('goldenbraid_info.html',
{'info': "Not enougth data to add the feature"},
context_instance=RequestContext(request))
name = request_data['name']
vector_name = request_data['Vector']
used_parts = {'Vector': vector_name,
'part_1': request_data['part_1'],
'part_2': request_data['part_2']}
seq = assemble_parts(used_parts, ['part_1', 'part_2'])
props = {'Description': [request_data['description']],
'Reference': [request_data['reference']]}
temp_fhand = NamedTemporaryFile(prefix='{0}.'.format(seq.id), suffix='.gb')
temp_fhand.write(seq.format('gb'))
temp_fhand.flush()
temp_fhand.seek(0)
try:
feature = add_feature(name=name, type_name=MODULE_TYPE_NAME,
vector=vector_name, genbank=temp_fhand, props=props,
owner=request.user, is_public=False)
except IntegrityError as error:
print error
if 'feature already in db' in str(error):
# TODO choose a template
return render_to_response('feature_exists.html',
{},
context_instance=RequestContext(request))
else:
return HttpResponseServerError()
except Exception as error:
print error
return HttpResponseServerError(error)
# if everithing os fine we show the just added feature
return redirect(feature.url)
