Fixed panics during large file parsing #86
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Forgot the bot was an a-hole, let me try to get those tests.... |
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@TimothyStiles I think your bot is bugged. Also, added in a test for location tags that are just single letters. I guess they happen sometimes, so are added in. I implemented that in one of the test files, which is why it increased the coverage. |
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Code Climate has analyzed commit d41459a and detected 1 issue on this pull request. Here's the issue category breakdown:
The test coverage on the diff in this pull request is 100.0% (95% is the threshold). This pull request will bring the total coverage in the repository to 96.8% (0.0% change). View more on Code Climate. |
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This PR fixes the parsing issues when it comes to big' ole real-life GenbankFlatFiles.
Note: I have no idea WHY exactly it fixed them all. Basically, all I did was add length checks in 4 places:
quickMetaCheck(if len(line) == 0, flag is false)quickSubMetaCheck(if len(line) == 0, flag is false)check if len(startEndSplit) is > 1 before doing
end, _ = strconv.Atoi(partialRegex.ReplaceAllString(startEndSplit[1], ""))finally, check if there is still line to parse over when trying to find paratheses in
switch expression[firstInnerParentheses+i]. Apparently, sometimes there ain't?And commented out a line of code
attributeValue = strings.TrimSpace(attributeSplit[1])I am not sure why this line is added - it is completely untested, and if you actually encounter it the system panics.
In particular, I tested with the following genbank file https://siasky.net/AABxAejn_kkw0H5O8ECVdPhFuMXy1uib_Z8B5JE5DctSuQ
It is pretty large, so I didn't actually push it to the main branch. It also takes quite a few seconds to parse, so there is that too.