def get_multipartite_form(multi_type, user):
'It returns a form for the given multipartite'
form_fields = OrderedDict()
part_defs = PARTS_TO_ASSEMBLE[multi_type]
for parts in part_defs:
features = Feature.objects.filter(type__name=parts[0],
prefix=parts[1],
suffix=parts[2])
features = filter_feature_by_user_perms(features, user)
choices = features_to_choices(features)
name = parts[0]
form_fields[name] = forms.CharField(max_length=100,
widget=Select(choices=choices))
# last we need to add the vector to the form
vector_choices = get_vector_choices(user)
form_fields[VECTOR_TYPE_NAME] = forms.CharField(max_length=100,
widget=Select(choices=vector_choices))
form = type('MultiPartiteForm', (forms.BaseForm,),
{'base_fields': form_fields})
for field_name in form_fields.keys():
setattr(form, 'clean_{0}'.format(field_name),
create_feature_validator(field_name))
return form
def get_bipart_vector_choices(part_uniquename, user):
part = Feature.objects.get(uniquename=part_uniquename)
part_enzyme_out = part.enzyme_out[0]
vectors = Feature.objects.filter(type__name=VECTOR_TYPE_NAME)
vectors = vectors.filter(featureprop__type__name=ENZYME_IN_TYPE_NAME,
featureprop__value=part_enzyme_out)
vectors = filter_feature_by_user_perms(vectors, user)
return _vectors_to_choice(vectors)
def get_part1_choice(user):
_bi_parts = Feature.objects.filter(type__name__in=BIPARTITE_ALLOWED_PARTS)
_parts = _bi_parts.filter(prefix=SITE_A, suffix=SITE_C)
_parts = filter_feature_by_user_perms(_parts, user)
parts_forw = _parts.filter(vector__prefix=SITE_B, vector__suffix=SITE_A)
parts_rev = _parts.filter(vector__prefix=Seq(SITE_A).reverse_complement(),
vector__suffix=Seq(SITE_B).reverse_complement())
part_forw_choices = features_to_choices(parts_forw, blank_line=False)
part_rev_choices = features_to_choices(parts_rev, blank_line=False)
part_choices = (('', ''),
('Forward parts', part_forw_choices),
('Reverse parts', part_rev_choices))
return part_choices
def get_part2_choices(part1_uniquename, user):
part1 = Feature.objects.get(uniquename=part1_uniquename)
part1_enzyme_out = part1.enzyme_out
bi_parts = Feature.objects.filter(type__name__in=BIPARTITE_ALLOWED_PARTS)
parts = bi_parts.filter(prefix=SITE_C, suffix=SITE_B)
parts = filter_feature_by_user_perms(parts, user)
parts_forw = parts.filter(vector__prefix=SITE_B, vector__suffix=SITE_A)
parts_rev = parts.filter(vector__prefix=Seq(SITE_A).reverse_complement(),
vector__suffix=Seq(SITE_B).reverse_complement())
part_forw_choices = []
for part in parts_forw:
if part.enzyme_out == part1_enzyme_out:
uniquename = part.uniquename.encode('utf-8')
if part.name:
show = u'{0} - {1}'.format(uniquename, part.name)
else:
show = uniquename
part_forw_choices.append((uniquename, show))
part_rev_choices = []
for part in parts_rev:
if part.enzyme_out == part1_enzyme_out:
uniquename = part.uniquename.encode('utf-8')
if part.name:
show = u'{0} - {1}'.format(uniquename, part.name)
else:
show = uniquename
part_rev_choices.append((uniquename, show))
part_forw_choices = sorted(part_forw_choices, key=itemgetter(0))
part_rev_choices = sorted(part_rev_choices, key=itemgetter(0))
part_choices = (('', ''),
('Forward parts', part_forw_choices),
('Reverse parts', part_rev_choices))
return part_choices
def get_vector_choices(user):
vectors = Feature.objects.filter(type__name=VECTOR_TYPE_NAME)
vectors = filter_feature_by_user_perms(vectors, user)
vector_choices = _vectors_to_choice(vectors)
return vector_choices
def get_all_vectors_as_choices(user):
vectors = Feature.objects.filter(type__name=VECTOR_TYPE_NAME)
vectors = filter_feature_by_user_perms(vectors, user)
return features_to_choices(vectors, blank_line=True)
