def test_combinations_of_deps():
graph = quoted_data(
'reactant(a,1;c,2;b,3;d,3). reaction(1;2;3). product(b,1;d,2;e,3).')
# utils.render_network(graph, 'todel.png') # uncomment to help debugging
expected_seeds_sets = {
frozenset('ac'),
frozenset('ad'),
frozenset('bc'),
frozenset('bd')
}
assert expected_seeds_sets == set(
search_seeds(graph, forbidden_seeds='e', targets='e'))
assert expected_seeds_sets == set(
search_seeds(graph,
forbidden_seeds='e',
targets='e',
compute_optimal_solutions=True))
assert {frozenset('abcd')} == set(
search_seeds(graph,
forbidden_seeds='e',
targets='e',
enum_mode='union'))
assert {frozenset()} == set(
search_seeds(graph,
forbidden_seeds='e',
targets='e',
enum_mode='intersection'))
def test_forbidden_intermediate_nodes_parallelized():
graph = quoted_data('reactant((a;b;c),1). product(d,1). reaction(1).'
'reactant(d,2). product(e,2). reaction(2).'
'reactant((m;n;o),3). product(e,3). reaction(3).')
utils.render_network(graph, 'todel.png') # uncomment to help debugging
seeds_sets = {frozenset('d'), frozenset('abc'), frozenset('mno')}
assert seeds_sets == set(search_seeds(graph, targets='e', explore_pareto=True, prerun=True))
seeds_sets = {frozenset('mno'), frozenset('abc'), frozenset('e')}
assert seeds_sets == set(search_seeds(graph, targets='e', forbidden_seeds='d', prerun=False))
def test_simple_reaction_chain():
"A -> C -> T: C cannot be chosen, because it does not maximize the scope as much as A"
graph = quoted_data('reactant(a,1). product(c,1). reaction(1). reactant(c,2). product(t,2). reaction(2).')
# utils.render_network(graph, 'todel.png') # uncomment to help debugging
seeds_sets = {frozenset('a')}
assert seeds_sets == set(search_seeds(graph, targets='t', forbidden_seeds='t', explore_pareto=True, greedy=True))
assert seeds_sets == set(search_seeds(graph, targets='t', explore_pareto=True, greedy=True))
seeds_sets = {frozenset('a')}
assert seeds_sets == set(search_seeds(graph, targets='t', forbidden_seeds='t', explore_pareto=True, greedy=False, verbose=True))
assert seeds_sets == set(search_seeds(graph, targets='t', explore_pareto=True, greedy=False))
def test_simple_reaction_chain_with_double_root():
"Same as previous, but with A+B -> C, allowing pareto front to choose either A+B or C."
graph = quoted_data('reactant((a;b),1). product(c,1). reaction(1). reactant(c,2). product(t,2). reaction(2).')
# utils.render_network(graph, 'todel.png') # uncomment to help debugging
seeds_sets = {frozenset('c'), frozenset('ab')}
assert seeds_sets == set(search_seeds(graph, targets='t', forbidden_seeds='t', explore_pareto=True, greedy=True))
seeds_sets = {frozenset('c'), frozenset('ab')}
assert seeds_sets == set(search_seeds(graph, targets='t', forbidden_seeds='t', explore_pareto=True, greedy=False))
seeds_sets = {frozenset('c')}
assert seeds_sets == set(search_seeds(graph, targets='t', forbidden_seeds='t', explore_pareto=True, greedy=False, verbose=True, compute_optimal_solutions=True))
def test_non_optimal_local():
graph = quoted_data(
'reactant((a;b),1). product(c,1). reaction(1). reactant((c;d),2). product(e,2). reaction(2). reactant(e,3). product(c,3). reaction(3).'
)
# utils.render_network(graph, 'todel.png') # uncomment to help debugging
expected_seeds_sets = {frozenset('abd'), frozenset('cd')}
assert expected_seeds_sets == set(
search_seeds(graph, forbidden_seeds='e', targets='e'))
expected_seeds_sets = {frozenset('cd')}
assert expected_seeds_sets == set(
search_seeds(graph,
start_seeds='d',
forbidden_seeds='e',
targets='e',
compute_optimal_solutions=True))
expected_seeds_sets = {frozenset('abd')}
assert expected_seeds_sets == set(
search_seeds(graph, forbidden_seeds='ce', targets='e'))
expected_seeds_sets = {frozenset('abd'), frozenset('adc')}
assert expected_seeds_sets == set(
search_seeds(graph, start_seeds='a', forbidden_seeds='e', targets='e'))
expected_seeds_sets = {frozenset('abcd')}
assert expected_seeds_sets == set(
search_seeds(graph,
start_seeds='a',
forbidden_seeds='e',
targets='e',
enum_mode='union'))
expected_seeds_sets = {frozenset('da')}
assert expected_seeds_sets == set(
search_seeds(graph,
start_seeds='a',
forbidden_seeds='e',
targets='e',
enum_mode='intersection'))
expected_seeds_sets = {frozenset('d')}
assert expected_seeds_sets == set(
search_seeds(graph,
forbidden_seeds='e',
targets='e',
enum_mode='intersection',
compute_optimal_solutions=False))
expected_seeds_sets = {frozenset('dc')}
assert expected_seeds_sets == set(
search_seeds(graph,
forbidden_seeds='e',
targets='e',
enum_mode='intersection',
compute_optimal_solutions=True))
assert expected_seeds_sets == set(
search_seeds(graph,
forbidden_seeds='e',
targets='e',
enum_mode='intersection',
compute_optimal_solutions=True,
greedy=True))
def test_simple_division():
graph = quoted_data('reactant(a,1). product(d,1). reaction(1).'
'reactant(c,2). product(e,2). reaction(2).'
'reactant(b,3). product((d;e),3). reaction(3).')
# utils.render_network(graph, 'todel.png') # uncomment to help debugging
expected_seeds_sets = {frozenset('ac'), frozenset('b')}
assert expected_seeds_sets == set(
search_seeds(graph, targets='de', forbidden_seeds='de'))
expected_seeds_sets = {frozenset('b')}
assert expected_seeds_sets == set(
search_seeds(graph,
targets='de',
forbidden_seeds='de',
compute_optimal_solutions=True))
def test_impossible_case():
"the code should return nothing when no solution is found, or raise ValueError when dubious question is asked"
graph = quoted_data(
'reactant((a;b),1). product((d;e),1). reaction(1). reactant((b;c),2). product((e;f),2). reaction(2).'
)
# utils.render_network(graph, 'todel.png') # uncomment to help debugging
assert not tuple(search_seeds(
graph, forbidden_seeds='a')) # impossible to activate a without a
assert not tuple(
search_seeds(graph, forbidden_seeds={'a', 'd'}, targets={'d'}))
with pytest.raises(ValueError):
list(
search_seeds(graph,
start_seeds='a',
forbidden_seeds='a',
targets='d'))
def test_long_reaction_chain():
"L -> O -> N -> G -> E -> R: only L can be chosen, because it maximizes the scope"
graph = quoted_data('reactant(l,1). product(o,1). reaction(1).'
'reactant(o,2). product(n,2). reaction(2).'
'reactant(n,3). product(g,3). reaction(3).'
'reactant(g,4). product(e,4). reaction(4).'
'reactant(e,5). product(r,5). reaction(5).')
# utils.render_network(graph, 'todel.png') # uncomment to help debugging
seeds_sets = {frozenset('l')}
assert seeds_sets == set(search_seeds(graph, prerun=False))
assert seeds_sets == set(search_seeds(graph, targets='r', explore_pareto=True, greedy=True, prerun=False))
assert seeds_sets == set(search_seeds(graph, targets='r', explore_pareto=True, greedy=False, prerun=False))
# Proof that the forbidden_seeds support has hard-to-manage side-effects:
seeds_sets = {frozenset('o')}
assert seeds_sets == set(search_seeds(graph, targets='r', forbidden_seeds='l', explore_pareto=True, greedy=True, prerun=False))
# If prerun is forgot, this one will fail, because no model is generated:
assert seeds_sets == set(search_seeds(graph, targets='r', forbidden_seeds='l', explore_pareto=True, greedy=False, prerun=True))
def test_infinite_loop_of_hypothesis():
graph = quoted_data('reactant((a;c),1). product(b,1). reaction(1).'
'reactant((b;d),2). product(c,2). reaction(2).')
# utils.render_network(graph, 'todel.png') # uncomment to help debugging
expected_seeds_sets = {frozenset('bd')}
assert expected_seeds_sets == set(
search_seeds(graph,
targets='c',
explore_pareto=True,
forbidden_seeds='c'))
expected_seeds_sets = {frozenset('bd'), frozenset('c')}
assert expected_seeds_sets == set(
search_seeds(graph, targets='c', explore_pareto=True))
expected_seeds_sets = {frozenset('bd'), frozenset('c')}
assert expected_seeds_sets == set(
search_seeds(graph, targets='c', explore_pareto=True))
def test_hierarchical_case():
graph = quoted_data(
'reactant((a;b),1). product(c,1). reaction(1). reactant(a,2). product(e,2). reaction(2). reactant((d;e),3). product(b,3). reaction(3).'
)
# utils.render_network(graph, 'todel.png') # uncomment to help debugging
expected_seeds_sets = {frozenset('ab'), frozenset('ad')}
assert expected_seeds_sets == set(
search_seeds(graph, forbidden_seeds='c', targets='c'))
expected_seeds_sets = {frozenset('c')}
assert expected_seeds_sets == set(
search_seeds(graph, targets='c', compute_optimal_solutions=True))
expected_seeds_sets = {
frozenset('ab'),
frozenset('ad'),
frozenset('bc'),
frozenset('cde')
}
assert expected_seeds_sets == set(search_seeds(graph, targets='bc'))
expected_seeds_sets = {frozenset('abcde')}
assert expected_seeds_sets == set(
search_seeds(graph, targets='bc', enum_mode='union'))
expected_seeds_sets = {frozenset('ab'), frozenset('ad'), frozenset('bc')}
assert expected_seeds_sets == set(
search_seeds(graph, targets='bc', compute_optimal_solutions=True))
expected_seeds_sets = {frozenset('abcde')}
assert expected_seeds_sets == set(
search_seeds(graph,
targets='bc',
compute_optimal_solutions=True,
enum_mode='union'))
assert expected_seeds_sets == set(
search_seeds(graph,
targets='bc',
compute_optimal_solutions=False,
enum_mode='union'))
expected_seeds_sets = {frozenset()}
assert expected_seeds_sets == set(
search_seeds(graph,
targets='bc',
compute_optimal_solutions=True,
enum_mode='intersection'))
assert expected_seeds_sets == set(
search_seeds(graph,
targets='bc',
compute_optimal_solutions=False,
enum_mode='intersection'))
def test_double_yielder():
graph = quoted_data('reactant(a,1). product(c,1). reaction(1).'
'reactant(a,2). product(d,2). reaction(2).'
'reactant(b,3). product(c,3). reaction(3).'
'reactant(c,r3). product(b,r3). reaction(r3).'
'reactant(d,4). product(e,4). reaction(4).'
'reactant(e,r4). product(d,r4). reaction(r4).'
'reactant(e,5). product(g,5). reaction(5).'
'reactant(b,6). product(f,6). reaction(6).')
graph_7 = graph + quoted_data('reactant(d,7). product(c,7). reaction(7).')
# utils.render_network(graph_7 + 'dot_property("7",style,dashed).', 'todel.png') # uncomment to help debugging
expected_seeds_sets = {
frozenset('a'),
frozenset('cd'),
frozenset('ce'),
frozenset('bd'),
frozenset('be')
}
assert expected_seeds_sets == set(
search_seeds(graph, targets='fg', forbidden_seeds='fg'))
expected_seeds_sets = {frozenset('a'), frozenset('d'), frozenset('e')}
assert expected_seeds_sets == set(
search_seeds(graph_7, targets='fg', forbidden_seeds='fg'))
# optimal search
expected_seeds_sets = {frozenset('a')}
assert expected_seeds_sets == set(
search_seeds(graph,
targets='fg',
forbidden_seeds='de',
compute_optimal_solutions=True))
expected_seeds_sets = {frozenset('a'), frozenset('d'), frozenset('e')}
assert expected_seeds_sets == set(
search_seeds(graph_7,
targets='fg',
forbidden_seeds='fg',
compute_optimal_solutions=True))
def test_forbidden_intermediate_nodes():
"Test the handling of middle SCC that are completely forbidden"
graph = quoted_data('reactant((a;b;c),1). product(d,1). reaction(1).'
'reactant(d,2). product(e,2). reaction(2).')
# utils.render_network(graph, 'todel.png') # uncomment to help debugging
seeds_sets = {frozenset('e'), frozenset('abc'), frozenset('ae'), frozenset('be'), frozenset('ce')}
assert seeds_sets == set(search_seeds(graph, targets='e', forbidden_seeds='d', explore_pareto=True, greedy=True, prerun=False))
assert seeds_sets == set(search_seeds(graph, targets='e', forbidden_seeds='d', explore_pareto=True, greedy=True, prerun=False))
seeds_sets = {frozenset('e')}
assert seeds_sets == set(search_seeds(graph, targets='e', forbidden_seeds='d', prerun=False, compute_optimal_solutions=True))
seeds_sets = {frozenset('d'), frozenset('abc')}
assert seeds_sets == set(search_seeds(graph, targets='e', explore_pareto=True, prerun=True)) # d as seeds covers more metabolites + less targets as seeds
assert seeds_sets == set(search_seeds(graph, targets='e', explore_pareto=True, prerun=False))
seeds_sets = {frozenset('e'), frozenset('abc')}
assert seeds_sets == set(search_seeds(graph, targets='e', forbidden_seeds='d', prerun=False))
seeds_sets = {frozenset('e'), frozenset('abc')}
assert seeds_sets == set(search_seeds(graph, targets='e', forbidden_seeds='d', explore_pareto=True, greedy=True, prerun=False, verbose=True))
assert seeds_sets == set(search_seeds(graph, targets='e', forbidden_seeds='d', explore_pareto=True, prerun=True, verbose=True))
def test_one_scc():
"""This show the local limits: whenever solutions are in the same SCC,
only the very best are yielded. As a consequence, both pareto and without
pareto loose some interesting (though non-optimal) solutions
This problem has been fixed by implementing iterative pareto.
(see last tests)
"""
graph = quoted_data("""reactant(a,1). product(b,1). reaction(1).
reactant((b;c),2). product(d,2). reaction(2).
reactant(d,3). product(a,3). reaction(3).
reactant((d;e),4). product(f,4). reaction(4).
reactant(f,5). product(c,5). reaction(5).""")
# utils.render_network(graph, 'todel.png') # uncomment to help debugging
expected_seeds_sets = {frozenset('d'), frozenset('de')} # 'af' would have been welcome, but does not cover as much as 'de'
assert expected_seeds_sets == set(search_seeds(graph, targets='d', explore_pareto=True, greedy=True, avoid_targets_as_seeds=True))
assert expected_seeds_sets == set(search_seeds(graph, targets='d', explore_pareto=True, greedy=True, avoid_targets_as_seeds=False)) # invariant
expected_seeds_sets = {frozenset('d')} # this is… optimized
assert expected_seeds_sets == set(search_seeds(graph, targets='d', explore_pareto=False))
# to get a real sens of diversity, we need to forbids the obvious solutions
# (here, just 'd', but it could be much more subtle).
expected_seeds_sets = {frozenset('ac'), frozenset('af'), frozenset('bc'), frozenset('bf')}
assert expected_seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='d', explore_pareto=False))
expected_seeds_sets = {frozenset('af'), frozenset('bf'), frozenset('ace'), frozenset('aef'), frozenset('bce'), frozenset('bef')}
assert expected_seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='d', explore_pareto=True, greedy=True))
# hence, this test ask a question: do another metric for the greedy search
# in an SCC is needed ? Probably.
# Something like a constraint providing *a maximal number/ratio of seed*.
# This is approached using a mix of iterative and pareto solution:
# while using greedy and pareto.
expected_seeds_sets = {frozenset('af'), frozenset('bf'), frozenset('ace'), frozenset('aef'), frozenset('bce'), frozenset('bef')}
assert expected_seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='d', explore_pareto=True, greedy=False, verbose=True,
compute_optimal_solutions=False, filter_included_solutions=False))
expected_seeds_sets = {frozenset('af'), frozenset('bf'), frozenset('ace'), frozenset('bce')}
assert expected_seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='d', explore_pareto=True, greedy=False, verbose=True,
compute_optimal_solutions=False, filter_included_solutions=True))
expected_seeds_sets = {frozenset('af'), frozenset('bf')}
assert expected_seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='d', explore_pareto=True, greedy=False, verbose=True,
compute_optimal_solutions=True, filter_included_solutions=True))
def test_forbidden_sources():
"Test the handling of root SCC that are completely forbidden"
graph = quoted_data('reactant(a,1). product(b,1). reaction(1).'
'reactant(b,2). product(a,2). reaction(2).'
'reactant(b,3). product(c,3). reaction(3).'
'reactant(c,4). product(d,4). reaction(4).')
# utils.render_network(graph, 'todel.png') # uncomment to help debugging
seeds_sets = {frozenset('a'), frozenset('b')}
assert seeds_sets == set(search_seeds(graph))
assert seeds_sets == set(search_seeds(graph, greedy=True))
assert seeds_sets == set(search_seeds(graph, targets='d', explore_pareto=True))
seeds_sets = {frozenset('a'), frozenset('b'), frozenset('d')}
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='c', greedy=True))
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='c'))
seeds_sets = {frozenset('c'), frozenset('d')}
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='ab', greedy=True))
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='ab'))
seeds_sets = {frozenset('c')}
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='abd', greedy=True))
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='abd'))
seeds_sets = {frozenset('d')}
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='abc', greedy=True))
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='abc'))
seeds_sets = set()
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='abcd', greedy=True))
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='abcd'))
# But with forbidden seeds, it's not that obvious:
# once arrived at SCC a (containing a and b), it is impossible to do anything.
seeds_sets = {frozenset('a'), frozenset('b')}
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='d', explore_pareto=True, greedy=True))
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='d', explore_pareto=True))
seeds_sets = {frozenset('a')}
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='b', explore_pareto=True, greedy=True))
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='b', explore_pareto=True, compute_optimal_solutions=True))
# seeds_sets = {frozenset('c'), frozenset('a')} # pareto exploration find optimals before compute_optimal_solutions post-process
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='b', explore_pareto=True, compute_optimal_solutions=False))
seeds_sets = {frozenset('b')}
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='a', explore_pareto=True, greedy=True))
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='a', explore_pareto=True, compute_optimal_solutions=True))
# seeds_sets = {frozenset('c'), frozenset('b')} # pareto exploration find optimals before compute_optimal_solutions post-process
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='a', explore_pareto=True, compute_optimal_solutions=False))
seeds_sets = {frozenset('c')}
assert seeds_sets == set(search_seeds(graph, targets='d', forbidden_seeds='ab', explore_pareto=True))
def test_lattice_reaction():
graph = quoted_data(
'reactant((a;b),1). product((d;e),1). reaction(1). reactant((b;c),2). product((e;f),2). reaction(2).'
)
# utils.render_network(graph, 'todel.png') # uncomment to help debugging
expected_seeds_sets = {frozenset('bc'), frozenset('fab')}
assert expected_seeds_sets == set(
search_seeds(graph, targets='ef', forbidden_seeds='e'))
expected_seeds_sets = {frozenset('bc')}
assert expected_seeds_sets == set(
search_seeds(graph,
targets='ef',
forbidden_seeds='e',
compute_optimal_solutions=True))
assert expected_seeds_sets == set(
search_seeds(graph, targets='f', forbidden_seeds='f'))
expected_seeds_sets = {frozenset('ab'), frozenset('de'), frozenset('dbc')}
assert expected_seeds_sets == set(search_seeds(graph, targets='de'))
expected_seeds_sets = {frozenset('ab'), frozenset('de')}
assert expected_seeds_sets == set(
search_seeds(graph, targets='de', compute_optimal_solutions=True))
expected_seeds_sets = {frozenset('ab')}
assert expected_seeds_sets == set(
search_seeds(graph, targets='d', forbidden_seeds='d'))
expected_seeds_sets = {frozenset('ab'), frozenset('bc')}
assert expected_seeds_sets == set(
search_seeds(graph, targets='e', forbidden_seeds='e'))
assert {frozenset('abc')} == set(
search_seeds(graph,
targets='e',
forbidden_seeds='e',
enum_mode='union'))
assert {frozenset('b')} == set(
search_seeds(graph,
targets='e',
forbidden_seeds='e',
enum_mode='intersection'))
assert {frozenset('abc')
} == set(search_seeds(graph, targets='def', forbidden_seeds='def'))
assert {frozenset('ab')
} == set(search_seeds(graph, targets='e', forbidden_seeds='ce'))
def test_network_example():
seeds_sets = set(search_seeds(graph))
# utils.render_network(graph, 'todel.png') # uncomment to help debugging
assert seeds_sets == expected_seeds_sets
def test_toy1():
"Usage of only graph_filename as parameter, enabling the use of networkx to search for SCCs"
seeds_sets = set(predator.search_seeds(graph_filename='./networks/toy_1.sbml'))
assert seeds_sets == set(map(frozenset, ({'s', 'b'}, {'s', 'c'}, {'s', 'd'}, {'s', 'e'})))