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Fix security issues - #3489
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jeromekelleher wants to merge 5 commits into
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Fix security issues#3489jeromekelleher wants to merge 5 commits into
jeromekelleher wants to merge 5 commits into
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Sample and ancestor IDs equal to the number of nodes were accepted, leading to out-of-bounds accesses on node-sized arrays. Closes tskit-dev#3484
Sample IDs equal to the number of nodes were accepted by both ibd_within and ibd_between, leading to an out-of-bounds write on the sample_set_id array. Closes tskit-dev#3485
delete_older used edge parents, mutation nodes and mutation parents as array indexes without validation, after it had already started rewriting the tables. Invalid references led to out-of-bounds reads and partially modified tables. Closes tskit-dev#3486
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #3489 +/- ##
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- Coverage 91.68% 91.67% -0.02%
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Files 38 38
Lines 32232 32240 +8
Branches 5153 5155 +2
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+ Hits 29553 29555 +2
- Misses 2346 2350 +4
- Partials 333 335 +2
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The table metadata schema tests computed the length of example2 using strlen(example), reading past the end of the shorter string. test_zero_edges passed a single tsk_id_t as the simplify node_map, which must have space for every input node.
The number of reference sets was used to compute an allocation size before being checked, so out-of-range values led to very large (or overflowing) allocation requests before the error was returned.
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Also tacked on a couple of extra fixes which came up while looking at this. |
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Fixes a handful of security issues reported by @gregorgorjanc - Codex was spot on.
I'm quite pleased that this is all that security audits are surfacing - go tskit!