Avoid assertion error crashes during import #4829
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@mandawilson @averyniceday @sheridancbio I recommend viewing the diff without the whitespace changes |
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averyniceday
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Throws exception when a sample ID is not known to database AND is not a normal sample. Otherwise, assertion failure causes importer to crash and does not log the issue. Signed-off-by: Angelica Ochoa <aochoa4230@gmail.com>
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Great. This allows exceptions to be caught be a client java application (such as the mskcc importer), rather than having AssertionErrors terminate the client program.
- also : very glad that github offers the "Hide Whitespace Changes" option when doing PR review 👏
| @@ -56,7 +56,7 @@ | |||
| public static final String CNA_VALUE_ZERO = "0"; | |||
| private HashSet<Long> importSetOfGenes = new HashSet<Long>(); | |||
| private HashSet<Integer> importedGeneticEntitySet = new HashSet<>(); | |||
| private File mutationFile; | |||
| private File dataFile; | |||
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Throws exception when a sample ID is not known to database AND is not a normal sample. Otherwise, assertion failure causes importer to crash and does not log the issue.
Signed-off-by: Angelica Ochoa aochoa4230@gmail.com
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