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Fixing check for shared history in union #904

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Merged
merged 1 commit into from
Nov 9, 2020
Merged

Fixing check for shared history in union #904

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12 changes: 10 additions & 2 deletions c/tests/test_tables.c
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Original file line number Diff line number Diff line change
Expand Up @@ -5074,6 +5074,8 @@ test_table_collection_union(void)
tsk_table_collection_t tables_empty;
tsk_table_collection_t tables_copy;
tsk_id_t node_mapping[3];
char example_metadata[100] = "An example of metadata with unicode 🎄🌳🌴🌲🎋";
tsk_size_t example_metadata_length = (tsk_size_t) strlen(example_metadata);

memset(node_mapping, 0xff, sizeof(node_mapping));

Expand All @@ -5087,8 +5089,14 @@ test_table_collection_union(void)
CU_ASSERT_EQUAL_FATAL(ret, 0);

// does not error on empty tables
ret = tsk_table_collection_union(
&tables, &tables_empty, node_mapping, TSK_UNION_NO_CHECK_SHARED);
ret = tsk_table_collection_union(&tables, &tables_empty, node_mapping, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

// does not error on empty tables but that differ on top level metadata
ret = tsk_table_collection_set_metadata(
&tables, example_metadata, example_metadata_length);
CU_ASSERT_EQUAL(ret, 0);
ret = tsk_table_collection_union(&tables, &tables_empty, node_mapping, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

// three nodes, two pop, three ind, two edge, two site, two mut
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11 changes: 2 additions & 9 deletions c/tskit/tables.c
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Original file line number Diff line number Diff line change
Expand Up @@ -9256,14 +9256,6 @@ tsk_check_subset_equality(tsk_table_collection_t *self,
if (ret != 0) {
goto out;
}
ret = tsk_provenance_table_clear(&other_copy.provenances);
if (ret != 0) {
goto out;
}
ret = tsk_provenance_table_clear(&self_copy.provenances);
if (ret != 0) {
goto out;
}
ret = tsk_table_collection_subset(&self_copy, self_nodes, num_shared_nodes);
if (ret != 0) {
goto out;
Expand All @@ -9272,7 +9264,8 @@ tsk_check_subset_equality(tsk_table_collection_t *self,
if (ret != 0) {
goto out;
}
if (!tsk_table_collection_equals(&self_copy, &other_copy, 0)) {
if (!tsk_table_collection_equals(&self_copy, &other_copy,
TSK_CMP_IGNORE_TS_METADATA | TSK_CMP_IGNORE_PROVENANCE)) {
ret = TSK_ERR_UNION_DIFF_HISTORIES;
goto out;
}
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14 changes: 9 additions & 5 deletions python/tests/test_tables.py
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Expand Up @@ -3216,6 +3216,12 @@ def split_example(self, ts, T):
i if i < len(shared_nodes) else tskit.NULL
for i in range(tables2.nodes.num_rows)
]
# adding some metadata to one of the tables
# union should disregard differences in metadata
tables1.metadata_schema = tskit.MetadataSchema(
{"codec": "json", "type": "object"}
)
tables1.metadata = {"hello": "world"}
return tables1, tables2, node_mapping

def verify_union_equality(self, tables, other, node_mapping, add_populations=True):
Expand All @@ -3225,7 +3231,7 @@ def verify_union_equality(self, tables, other, node_mapping, add_populations=Tru
uni1.union(
other,
node_mapping,
record_provenance=False,
record_provenance=True,
add_populations=add_populations,
)
tsutil.py_union(
Expand All @@ -3235,15 +3241,13 @@ def verify_union_equality(self, tables, other, node_mapping, add_populations=Tru
record_provenance=False,
add_populations=add_populations,
)
assert uni1 == uni2
assert uni1.equals(uni2, ignore_ts_metadata=True, ignore_provenance=True)
# verifying that subsetting to original nodes return the same table
orig_nodes = [j for i, j in enumerate(node_mapping) if j != tskit.NULL]
uni1.subset(orig_nodes)
# subsetting tables just to make sure order is the same
tables.subset(orig_nodes)
uni1.provenances.clear()
tables.provenances.clear()
assert uni1 == tables
assert uni1.equals(tables, ignore_ts_metadata=True, ignore_provenance=True)

def test_noshared_example(self):
ts1 = self.get_msprime_example(sample_size=3, T=2, seed=9328)
Expand Down