Skip to content

Limit table size to TSK_MAX_ID #2337

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Jun 15, 2022
Merged

Limit table size to TSK_MAX_ID #2337

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 5 additions & 0 deletions c/CHANGELOG.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,11 @@
nodes of each node in the tree. (:user:`GertjanBisschop`, :issue:`2274`, :pr:`2316`)


**Changes**

- Reduce the maximum number of rows in a table by 1. This removes edge cases so that a ``tsk_id_t`` can be
used to count the number of rows. (:user:`benjeffery`, :issue:`2336`, :pr:`2337`)

--------------------
[1.0.0] - 2022-05-24
--------------------
Expand Down
18 changes: 9 additions & 9 deletions c/tests/test_tables.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5927,7 +5927,7 @@ test_table_expansion(void)

/*Extending by more rows than possible results in overflow*/
ret = tsk_individual_table_extend(
&tables.individuals, &tables2.individuals, TSK_MAX_ID + 1, NULL, 0);
&tables.individuals, &tables2.individuals, TSK_MAX_ID, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_TABLE_OVERFLOW);
CU_ASSERT_EQUAL_FATAL(tables.individuals.max_rows, 4194305);

Expand Down Expand Up @@ -5986,7 +5986,7 @@ test_table_expansion(void)
CU_ASSERT_EQUAL_FATAL(tables.nodes.max_rows, 4194305);

/*Extending by more rows than possible results in overflow*/
ret = tsk_node_table_extend(&tables.nodes, &tables2.nodes, TSK_MAX_ID + 1, NULL, 0);
ret = tsk_node_table_extend(&tables.nodes, &tables2.nodes, TSK_MAX_ID, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_TABLE_OVERFLOW);
CU_ASSERT_EQUAL_FATAL(tables.nodes.max_rows, 4194305);

Expand Down Expand Up @@ -6044,7 +6044,7 @@ test_table_expansion(void)
CU_ASSERT_EQUAL_FATAL(tables.edges.max_rows, 4194305);

/*Extending by more rows than possible results in overflow*/
ret = tsk_edge_table_extend(&tables.edges, &tables2.edges, TSK_MAX_ID + 1, NULL, 0);
ret = tsk_edge_table_extend(&tables.edges, &tables2.edges, TSK_MAX_ID, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_TABLE_OVERFLOW);
CU_ASSERT_EQUAL_FATAL(tables.edges.max_rows, 4194305);

Expand Down Expand Up @@ -6109,7 +6109,7 @@ test_table_expansion(void)

/*Extending by more rows than possible results in overflow*/
ret = tsk_migration_table_extend(
&tables.migrations, &tables2.migrations, TSK_MAX_ID + 1, NULL, 0);
&tables.migrations, &tables2.migrations, TSK_MAX_ID, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_TABLE_OVERFLOW);
CU_ASSERT_EQUAL_FATAL(tables.migrations.max_rows, 4194305);

Expand Down Expand Up @@ -6168,7 +6168,7 @@ test_table_expansion(void)
CU_ASSERT_EQUAL_FATAL(tables.sites.max_rows, 4194305);

/*Extending by more rows than possible results in overflow*/
ret = tsk_site_table_extend(&tables.sites, &tables2.sites, TSK_MAX_ID + 1, NULL, 0);
ret = tsk_site_table_extend(&tables.sites, &tables2.sites, TSK_MAX_ID, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_TABLE_OVERFLOW);
CU_ASSERT_EQUAL_FATAL(tables.sites.max_rows, 4194305);

Expand Down Expand Up @@ -6232,7 +6232,7 @@ test_table_expansion(void)

/*Extending by more rows than possible results in overflow*/
ret = tsk_mutation_table_extend(
&tables.mutations, &tables2.mutations, TSK_MAX_ID + 1, NULL, 0);
&tables.mutations, &tables2.mutations, TSK_MAX_ID, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_TABLE_OVERFLOW);
CU_ASSERT_EQUAL_FATAL(tables.mutations.max_rows, 4194305);

Expand Down Expand Up @@ -6298,7 +6298,7 @@ test_table_expansion(void)

/*Extending by more rows than possible results in overflow*/
ret = tsk_population_table_extend(
&tables.populations, &tables2.populations, TSK_MAX_ID + 1, NULL, 0);
&tables.populations, &tables2.populations, TSK_MAX_ID, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_TABLE_OVERFLOW);
CU_ASSERT_EQUAL_FATAL(tables.populations.max_rows, 4194305);

Expand Down Expand Up @@ -6364,7 +6364,7 @@ test_table_expansion(void)

/*Extending by more rows than possible results in overflow*/
ret = tsk_provenance_table_extend(
&tables.provenances, &tables2.provenances, TSK_MAX_ID + 1, NULL, 0);
&tables.provenances, &tables2.provenances, TSK_MAX_ID, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_TABLE_OVERFLOW);
CU_ASSERT_EQUAL_FATAL(tables.provenances.max_rows, 4194305);

Expand Down Expand Up @@ -8576,7 +8576,7 @@ test_table_overflow(void)
int ret;
tsk_id_t ret_id;
tsk_table_collection_t tables;
tsk_size_t max_rows = ((tsk_size_t) TSK_MAX_ID) + 1;
tsk_size_t max_rows = ((tsk_size_t) TSK_MAX_ID);

ret = tsk_table_collection_init(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
Expand Down
13 changes: 8 additions & 5 deletions c/tskit/tables.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,13 +79,14 @@ typedef struct {
} write_table_ragged_col_t;

/* Returns true if adding the specified number of rows would result in overflow.
* Tables can support indexes from 0 to TSK_MAX_ID, and therefore have at most
* TSK_MAX_ID + 1 rows */
* Tables can support indexes from 0 to TSK_MAX_ID, and therefore could have at most
* TSK_MAX_ID + 1 rows. However we limit to TSK_MAX_ID rows so that counts of rows
* can fit in a tsk_id_t. */
static bool
check_table_overflow(tsk_size_t current_size, tsk_size_t additional_rows)
{
tsk_size_t max_val = TSK_MAX_ID + (tsk_size_t) 1;
return current_size > (max_val - additional_rows);
tsk_size_t max_val = TSK_MAX_ID;
return additional_rows > max_val || current_size > (max_val - additional_rows);
}

/* Returns true if adding the specified number of elements would result in overflow
Expand All @@ -94,7 +95,9 @@ check_table_overflow(tsk_size_t current_size, tsk_size_t additional_rows)
static bool
check_offset_overflow(tsk_size_t current_size, tsk_size_t additional_elements)
{
return current_size > (TSK_MAX_SIZE - additional_elements);
tsk_size_t max_val = TSK_MAX_SIZE;
return additional_elements > max_val
|| current_size > (max_val - additional_elements);
}

#define TSK_NUM_ROWS_UNSET ((tsk_size_t) -1)
Expand Down