Fix python segfault when using an invalid Aligner - #1344
Open
blawrence-ont wants to merge 2 commits into
Open
blawrence-ont wants to merge 2 commits into
blawrence-ont wants to merge 2 commits into
Conversation
Trying to use autocomplete on an Aligner that wasn't valid, for example to debug it, would crash the REPL due to these missing checks. To fix that add some checks that were missing. Technically returning None is the same as returning nothing, but it's best to be consistent.
This was showing up as importable under mappy, ie the following worked: >>> from mappy import sys
This branch has not been deployed
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Similar to #1195, we recently saw python segfault due to malformed paths.
Simple repro case in the REPL is:
where the segfault occurred on line 3 when pressing tab after the
.to display attributes of the object. The same crash occurs if trying to access the fields with missingNULLchecks, iealigner.n_seq.Note that #1195 is probably a better fix if a behaviour change is allowed and would avoid the need for any
NULLchecks.See commit descriptions for more details.