Changes to report logic: STRY0017737 #188
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test with additional missing report needed data needed e.g. checkm disabled |
We cannot get CheckM to run in current tests so it is currently disabled showing 3/4 passed tests. If CheckM is enabled we see 4/4 passed tests, it is unclear if users would like to see the number of passed tests reflect skipped tests or not and we should follow up on this later. E.g. if CheckM is skipped the user would see 3/3 passed tests in our examples. |
apetkau
requested changes
Sep 10, 2025
lib/ReportFunctions.groovy
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| class ReportFunctions{ | ||
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| /* | ||
| enum FuncType{ |
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Could you remove this commented out bit of code.
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fixed in: e67cbdd
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| def qual_message = [] | ||
| def failed_p = false | ||
| //def failed_p = false |
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If this is now unused could you remove it.
| check_failed, | ||
| check_ignored) = this.contig_qc_func(qual_data, metric, qc_message) | ||
| break; | ||
| } |
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Could you add a default case here that raises an exception about an invalid FuncType (though I suspect you would likely also get an exception raised when casting the string to the enum FuncType anyways).
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fixed in: e67cbdd
lib/ReportFunctions.groovy
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| resequence, | ||
| failed_p, | ||
| check_failed, | ||
| check_ignored) = this.generic_qc_func(qual_data, metric, qc_message) |
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I would use ReportFunctions.generic_qc_func() to call the function (or just generic_qc_func()) since these are static functions and this is meant to refer to the particular instance of a class (for non-static functions). Though it seems like it works anyways like how you have things.
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fixed in: e67cbdd
lib/ReportFunctions.groovy
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| resequence = 1 | ||
| failed_p = true | ||
| checks_failed = 1 | ||
| //return [checks, reisolate, resequence, failed_p, checks_failed, checks_ignored] |
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fixed in: e67cbdd
lib/ReportFunctions.groovy
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| resequence, | ||
| failed_p, | ||
| check_failed, | ||
| check_ignored) = this.generic_qc_func(qual_data, metric, qc_message) |
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Is GENERIC and AUTOFAIL meant to run identical code?
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nope, a separate method should be run good catch!
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fixed in: e67cbdd
lib/ReportFunctions.groovy
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| class ReportFunctions{ |
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Could you maybe run the VSCode formatter on this file to clean up whitespace, etc?
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fixed in: e67cbdd
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The autofail function needs to be tested better, e.g. a failing result needs to be passed to checkM |
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The changes in this PR are performed to reflect what is listed in STRY0017737, however the implementation of how the work is done has been altered.
Acceptance Criteria: