def build_hierarchy():
r"""Return hierarchy with this structure:
a
/ \
b c
/ \ / \
d e f
/ \ / \ / \
g h i j
"""
edges = [
("a", "b"),
("a", "c"),
("b", "d"),
("b", "e"),
("c", "e"),
("c", "f"),
("d", "g"),
("d", "h"),
("e", "h"),
("e", "i"),
("f", "i"),
("f", "j"),
]
return Hierarchy("a", edges)
def test_roundtrip_examples(subtests):
# tree has this structure:
#
# ┌--0--┐
# | |
# ┌--1--┌--2--┐
# | | |
# ┌-3-┐ ┌-4-┐ ┌-5-┐
# | | | | | |
# 6 7 8 9 10 11
edges = [
("0", "1"),
("0", "2"),
("1", "3"),
("1", "4"),
("2", "4"),
("2", "5"),
("3", "6"),
("3", "7"),
("4", "8"),
("4", "9"),
("5", "10"),
("5", "11"),
]
hierarchy = Hierarchy("0", edges)
for codes, query in [
# the root element
({"0"}, ["0"]),
# an intermediate element
({"2"}, ["2"]),
# a leaf element
({"8"}, ["8"]),
# everything under intermediate element, inclusive
({"2", "4", "5", "8", "9", "10", "11"}, ["2<"]),
# everything under intermediate element, exclusive
({"4", "5", "8", "9", "10", "11"}, ["4<", "5<"]),
# everything under intermediate element, except another intermediate element
({"2", "5", "8", "9", "10", "11"}, ["2<", "~4"]),
# everything under intermediate element, except leaf element
({"2", "4", "5", "9", "10", "11"}, ["2<", "~8"]),
# everything under root element, except intermediate element and its children (i)
({"0", "1", "2", "3", "4", "6", "7", "8", "9"}, ["0", "1<", "2"]),
# everything under root element, except intermediate element and its children (ii)
({"0", "1", "2", "3", "5", "6", "7", "10",
"11"}, ["0", "1", "2", "3<", "5<"]),
]:
with subtests.test(codes=codes, query=query):
defn1 = Definition.from_codes(codes, hierarchy)
assert sorted(str(r) for r in defn1.rules) == sorted(query)
assert defn1.codes(hierarchy) == codes
defn2 = Definition.from_query(query)
assert sorted(str(r) for r in defn2.rules) == sorted(query)
assert defn2.codes(hierarchy) == codes
def hierarchies(draw, size):
"""Build a Hierarchy with `size` nodes.
Based on an indea by @Zac-HD at https://github.com/HypothesisWorks/hypothesis/issues/2464.
"""
edges = []
for child_id in range(1, size):
for parent_id in draw(
st.sets(st.sampled_from(range(child_id)), min_size=1)):
edges.append((parent_id, child_id))
return Hierarchy("0", edges)
def update_code_statuses(*, codelist, updates):
code_to_status = dict(codelist.codes.values_list("code", "status"))
h = Hierarchy.from_codes(codelist.coding_system, list(code_to_status))
new_code_to_status = h.update_node_to_status(code_to_status, updates)
status_to_new_code = defaultdict(list)
for code, status in new_code_to_status.items():
status_to_new_code[status].append(code)
for status, codes in status_to_new_code.items():
codelist.codes.filter(code__in=codes).update(status=status)
logger.info("Updated Codelist Statuses", codelist_pk=codelist.pk)
def test_build_definition_rows():
# hierarchy has this structure:
#
# ┌--0--┐
# | |
# ┌--1--┌--2--┐
# | | |
# ┌-3-┐ ┌-4-┐ ┌-5-┐
# | | | | | |
# 6 7 8 9 10 11
edges = [
("0", "1"),
("0", "2"),
("1", "3"),
("1", "4"),
("2", "4"),
("2", "5"),
("3", "6"),
("3", "7"),
("4", "8"),
("4", "9"),
("5", "10"),
("5", "11"),
]
hierarchy = Hierarchy("0", edges)
# construct a hierarchy with 2, and all its descendants except 8
definition = Definition.from_codes({"2", "4", "5", "9", "10", "11"}, hierarchy)
# make a dummy coding system so we can do name lookup
dummy_coding_system = DummyCodingSystem()
rows = presenters.build_definition_rows(dummy_coding_system, hierarchy, definition)
# we expect only one row (with an exclusion for 8)
assert len(rows) == 1
row = rows[0]
assert row["code"] == "2"
assert row["all_descendants"]
# the only excluded code should be 8
assert len(row["excluded_descendants"]) == 1
excluded = row["excluded_descendants"][0]
assert excluded["code"] == "8"
def build_small_hierarchy():
r"""Return hierarchy with this structure:
a
/ \
b c
/ \ / \
d e f
"""
edges = [
("a", "b"),
("a", "c"),
("b", "d"),
("b", "e"),
("c", "e"),
("c", "f"),
]
return Hierarchy("a", edges)
def test_tree_tables(tennis_elbow_codelist):
cl = tennis_elbow_codelist
clv = cl.versions.get()
hierarchy = Hierarchy.from_codes(cl.coding_system, clv.codes)
ancestor_codes = hierarchy.filter_to_ultimate_ancestors(set(clv.codes))
codes_by_type = snomed.codes_by_type(ancestor_codes, hierarchy)
code_to_term = snomed.code_to_term(hierarchy.nodes)
# 128133004 (Disorder of elbow)
# ├ 429554009 (Arthropathy of elbow)
# │ └ 439656005 (Arthritis of elbow)
# │ └ 202855006 (Lateral epicondylitis)
# ├ 35185008 (Enthesopathy of elbow region)
# │ └ 73583000 (Epicondylitis)
# │ └ 202855006 (Lateral epicondylitis)
# └ 239964003 (Soft tissue lesion of elbow region)
assert presenters.tree_tables(codes_by_type, hierarchy, code_to_term) == [
{
"heading": "Disorder",
"rows": [
{
"code": "128133004",
"term": "Disorder of elbow",
"pipes": [],
},
{
"code": "429554009",
"term": "Arthropathy of elbow",
"pipes": ["├"],
},
{
"code": "439656005",
"term": "Arthritis of elbow",
"pipes": ["│", "└"],
},
{
"code": "202855006",
"term": "Lateral epicondylitis",
"pipes": ["│", " ", "└"],
},
{
"code": "35185008",
"term": "Enthesopathy of elbow region",
"pipes": ["├"],
},
{
"code": "73583000",
"term": "Epicondylitis",
"pipes": ["│", "└"],
},
{
"code": "202855006",
"term": "Lateral epicondylitis",
"pipes": ["│", " ", "└"],
},
{
"code": "239964003",
"term": "Soft tissue lesion of elbow region",
"pipes": ["└"],
},
],
}
]