def find_by_location(self, location, return_one=True, require_hit=True):
'''
TODO: Deal with whether to have a return one flag or always return
an array. To accept a solution as a query or to require a naked location.
I prefer to be able to have as much of the logic that is repeated
across different protocols handled by the underlying framework and thus
favor find(solution, by="location") or find(solution, by="components")
over location=sample['container']['location'];
find_by_location(location)[0].
'''
print location
hits = list(self.db.find({'container.location': location}))
if len(hits) > 1:
print 'Found more than one DB entry for location query.'
print 'Theres probably something wrong with your database.'
hit = hits[0]
if require_hit and (len(hits) == 0):
raise Exception(
'Did not find DB hit for query with require_hit enabled.')
stripped = strip_internal(hit)
s = Solution(**stripped)
s.update_units() # Note - this will fail if the thing being passed in
# has a dna concentration of unknown or string None...
return s
def find_by_location(self, location, return_one=True, require_hit=True):
'''
TODO: Deal with whether to have a return one flag or always return
an array. To accept a solution as a query or to require a naked location.
I prefer to be able to have as much of the logic that is repeated
across different protocols handled by the underlying framework and thus
favor find(solution, by="location") or find(solution, by="components")
over location=sample['container']['location'];
find_by_location(location)[0].
'''
print location
hits = list(self.db.find({'container.location': location}))
if len(hits) > 1:
print 'Found more than one DB entry for location query.'
print 'Theres probably something wrong with your database.'
hit = hits[0]
if require_hit and (len(hits) == 0):
raise Exception('Did not find DB hit for query with require_hit enabled.')
stripped = strip_internal(hit)
s = Solution(**stripped)
s.update_units() # Note - this will fail if the thing being passed in
# has a dna concentration of unknown or string None...
return s
class Reaction(object):
'''An individual reaction, which may be composed of multiple sub-reactions.
'''
def __init__(self, reactions=None, module=None, inputs=None, outputs=None,
solution=None, incubation=None, name=None, meta=None,
params=None, constraints=None):
self.reactions = reactions
self.module = module
self.inputs = inputs
self.outputs = outputs
self.name = name
self.solution = solution
self.incubation = incubation
self.meta = meta
self.params = params
self.constraints = constraints
if (solution is not None) and not isinstance(solution, Solution):
self.solution = Solution(**solution)
#print self.solution.components
if self.solution.components is not None:
self.solution.update_units()
if isinstance(reactions, list):
names = set()
for i,r in enumerate(reactions):
assert 'name' in r, 'Each reaction must have a name.'
assert r['name'] not in names, 'Found two reactions with the same name.'
names.add(r['name'])
self.reactions[i] = Reaction(**r)
if params is not None:
self.params = make_dottable_dict(params)
if inputs is not None:
if not isinstance(inputs, list):
inputs = [inputs]
for i, ipt in enumerate(inputs):
assert isinstance(ipt, dict), 'Reaction object tried to load an input but was passed something other than a dict: ' + str(ipt)
assert ('container' in ipt) and ('location' in ipt['container']), 'an input must have a container and location'
def named(self, name):
if isinstance(self.reactions, list):
for i,r in enumerate(self.reactions):
assert hasattr(r, 'name'), 'Found reaction without a name when looking for named reaction.'
if r.name == name:
return r
return None
class Reaction(object):
'''An individual reaction, which may be composed of multiple sub-reactions.
'''
def __init__(self,
reactions=None,
module=None,
inputs=None,
outputs=None,
solution=None,
incubation=None,
name=None,
meta=None,
params=None,
constraints=None):
self.reactions = reactions
self.module = module
self.inputs = inputs
self.outputs = outputs
self.name = name
self.solution = solution
self.incubation = incubation
self.meta = meta
self.params = params
self.constraints = constraints
if (solution is not None) and not isinstance(solution, Solution):
self.solution = Solution(**solution)
#print self.solution.components
if self.solution.components is not None:
self.solution.update_units()
if isinstance(reactions, list):
names = set()
for i, r in enumerate(reactions):
assert 'name' in r, 'Each reaction must have a name.'
assert r[
'name'] not in names, 'Found two reactions with the same name.'
names.add(r['name'])
self.reactions[i] = Reaction(**r)
if params is not None:
self.params = make_dottable_dict(params)
if inputs is not None:
if not isinstance(inputs, list):
inputs = [inputs]
for i, ipt in enumerate(inputs):
assert isinstance(
ipt, dict
), 'Reaction object tried to load an input but was passed something other than a dict: ' + str(
ipt)
assert ('container' in ipt) and (
'location' in ipt['container']
), 'an input must have a container and location'
def named(self, name):
if isinstance(self.reactions, list):
for i, r in enumerate(self.reactions):
assert hasattr(
r, 'name'
), 'Found reaction without a name when looking for named reaction.'
if r.name == name:
return r
return None