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unique atomic agents #105

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merged 3 commits into from
Mar 26, 2024
Merged

unique atomic agents #105

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dc0c94c
implement only unique name atomics in struct
Mar 20, 2024
be91482
test correction - non-unique atomics
Mar 21, 2024
49b36b0
test extended - (non)unique atomics in struct
Mar 21, 2024
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2 changes: 1 addition & 1 deletion Testing/objects_testing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@
# structure
s1 = StructureAgent("B", {a1})
s2 = StructureAgent("D", set())
s3 = StructureAgent("K", {a1, a3, a5})
s3 = StructureAgent("K", {a1, a3, a11})
s4 = StructureAgent("B", {a4})
s5 = StructureAgent("D", {a5, a6})
s6 = StructureAgent("K", set())
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13 changes: 11 additions & 2 deletions Testing/parsing/test_complex.py
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Expand Up @@ -6,12 +6,12 @@ def test_parser():
assert ret.success
assert ret.data.children[0] == objects.c1

ret = objects.rate_complex_parser.parse("B(T{s}).D().K(T{s},S{s},S{_})::cell")
ret = objects.rate_complex_parser.parse("B(T{s}).D().K(T{s},S{s},U{a})::cell")
assert ret.success
assert ret.data.children[0] == objects.c2

ret = objects.rate_complex_parser.parse(
"B(T{s}).K(T{s}, S{s}, S{_}).D(S{_},T{p})::cyt"
"B(T{s}).K(T{s}, S{s}, U{a}).D(S{_},T{p})::cyt"
)
assert ret.success
assert ret.data.children[0] == objects.c3
Expand Down Expand Up @@ -58,3 +58,12 @@ def test_parser():

ret = objects.rate_complex_parser.parse("B(T{s})::")
assert not ret.success

ret = objects.rate_complex_parser.parse("B(T{s}, T{_})::cell")
assert not ret.success

ret = objects.rate_complex_parser.parse("B(T{s}, T{s})::cell")
assert not ret.success

ret = objects.rate_complex_parser.parse("B(T{s}, T{a})::cell")
assert not ret.success
10 changes: 8 additions & 2 deletions Testing/parsing/test_side.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,13 +13,13 @@ def test_parser():
assert ret.data.to_side() == objects.side2

ret = objects.side_parser.parse(
"B(T{s})::cell + B(T{s}).D().K(T{s},S{s},S{_})::cell + B(T{s}).D().K(T{s},S{s},S{_})::cell"
"B(T{s})::cell + B(T{s}).D().K(T{s},S{s},U{a})::cell + B(T{s}).D().K(T{s},S{s},U{a})::cell"
)
assert ret.success
assert ret.data.to_side() == objects.side3

ret = objects.side_parser.parse(
"B(T{s})::cell + 2 B(T{s}).D().K(T{s},S{s},S{_})::cell"
"B(T{s})::cell + 2 B(T{s}).D().K(T{s},S{s},U{a})::cell"
)
assert ret.success
assert ret.data.to_side() == objects.side3
Expand Down Expand Up @@ -48,3 +48,9 @@ def test_parser():

ret = objects.side_parser.parse("B(T{s}")
assert not ret.success

# not unique atomics in structure
ret = objects.side_parser.parse(
"B(T{s})::cell + B(T{s}).D().K(T{s},S{s},S{_})::cell + B(T{s}).D().K(T{s},S{s},S{_})::cell"
)
assert not ret.success
5 changes: 4 additions & 1 deletion Testing/parsing/test_structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
def test_parser():
assert objects.structure_parser.parse("B(T{s})").data == objects.s1
assert objects.structure_parser.parse("D()").data == objects.s2
assert objects.structure_parser.parse("K(T{s}, S{s}, S{_})").data == objects.s3
assert objects.structure_parser.parse("K(T{s}, S{s}, U{a})").data == objects.s3
assert objects.structure_parser.parse("B(T{_})").data == objects.s4
assert objects.structure_parser.parse("D(S{_},T{p})").data == objects.s5
assert objects.structure_parser.parse("K()").data == objects.s6
Expand All @@ -18,3 +18,6 @@ def test_parser():
assert not objects.structure_parser.parse("[B(T{s})]").success
assert not objects.structure_parser.parse("").success
assert not objects.structure_parser.parse("B({s})").success
assert not objects.structure_parser.parse("B(S{s}, S{a})").success
assert not objects.structure_parser.parse("B(S{a}, S{a})").success
assert not objects.structure_parser.parse("B(S{_}, S{a})").success
16 changes: 12 additions & 4 deletions eBCSgen/Parsing/ParseBCSL.py
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Expand Up @@ -544,11 +544,19 @@ def atomic(self, matches):

def structure(self, matches):
name = str(matches[0].children[0])
if len(matches) > 1:
composition = set(matches[1].children)
return StructureAgent(name, composition)
else:
if len(matches) <= 1:
return StructureAgent(name, set())
atomic_names = set()
composition = set()
for atomic in matches[1].children:
if atomic.name in atomic_names:
raise ComplexParsingError(
f"Duplicate atomic agent in structure: {atomic.name}", matches
)
atomic_names.add(atomic.name)
composition.add(atomic)

return StructureAgent(name, composition)

def rate_complex(self, matches):
sequence = []
Expand Down
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