Changes to report logic: STRY0017737 #188
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,140 @@ | ||
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| class ReportFunctions { | ||
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| enum FuncType { | ||
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| GENERIC, | ||
| CONTIG, | ||
| READQUALITY, | ||
| AUTOFAIL, | ||
| COVERAGE | ||
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| } | ||
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| static def select_qc_func(java.util.LinkedHashMap qual_data, java.lang.String metric, java.util.ArrayList qc_message, java.util.LinkedHashMap meta_info, java.lang.String func) { | ||
| def check_failed = 0 | ||
| def reisolate = 0 | ||
| def resequence = 0 | ||
| def check_ignored = 0 | ||
| def failed_p = false | ||
| def checks = 0 | ||
| def function = func as FuncType | ||
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| switch (function) { | ||
| case FuncType.GENERIC: | ||
| (checks, | ||
| reisolate, | ||
| resequence, | ||
| failed_p, | ||
| check_failed, | ||
| check_ignored) = ReportFunctions.generic_qc_func(qual_data, metric, qc_message) | ||
| break | ||
| case FuncType.AUTOFAIL: | ||
| (checks, | ||
| reisolate, | ||
| resequence, | ||
| failed_p, | ||
| check_failed, | ||
| check_ignored) = ReportFunctions.autofail_reisolate(qual_data, metric, qc_message) | ||
| break | ||
| case FuncType.READQUALITY: | ||
| if (!meta_info.assembly) { | ||
| (checks, | ||
| reisolate, | ||
| resequence, | ||
| failed_p, | ||
| check_failed, | ||
| check_ignored) = ReportFunctions.generic_qc_func(qual_data, metric, qc_message) | ||
| } | ||
| break | ||
| case FuncType.COVERAGE: | ||
| if (!meta_info.assembly) { | ||
| (checks, | ||
| reisolate, | ||
| resequence, | ||
| failed_p, | ||
| check_failed, | ||
| check_ignored) = ReportFunctions.generic_qc_func(qual_data, metric, qc_message) | ||
| if (!failed_p && meta_info.downsampled) { | ||
| qc_message.add('The sample may have been downsampled too aggressively, if this is the cause please re-run sample with a different target depth.') | ||
| } | ||
| } | ||
| break | ||
| case FuncType.CONTIG: | ||
| (checks, | ||
| reisolate, | ||
| resequence, | ||
| failed_p, | ||
| check_failed, | ||
| check_ignored) = ReportFunctions.contig_qc_func(qual_data, metric, qc_message) | ||
| break | ||
| default: | ||
| throw NoSuchMethodExeption("No function for $func exists.") | ||
| } | ||
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| return [checks, reisolate, resequence, failed_p, check_failed, check_ignored] | ||
| } | ||
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| static def contig_qc_func(java.util.LinkedHashMap qual_data, java.lang.String metric, java.util.ArrayList qc_message) { | ||
| def checks_failed = 0 | ||
| def reisolate = 0 | ||
| def resequence = 0 | ||
| def checks_ignored = 0 | ||
| def failed_p = false | ||
| def checks = 0 | ||
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| if (qual_data && qual_data.containsKey(metric) && !qual_data[metric].status) { | ||
| checks_failed = 1 | ||
| failed_p = true | ||
| }else if (qual_data && (!qual_data.containsKey(metric) || !qual_data[metric].status)) { | ||
| checks_ignored = 1 | ||
| }else if (qual_data == null) { | ||
| checks_ignored = 1 | ||
| } | ||
| checks += 1 | ||
| return [checks, reisolate, resequence, failed_p, checks_failed, checks_ignored] | ||
| } | ||
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| static def generic_qc_func(java.util.LinkedHashMap qual_data, java.lang.String metric, java.util.ArrayList qc_message) { | ||
| def reisolate = 0 | ||
| def resequence = 0 | ||
| def failed_p = false | ||
| def checks_failed = 0 | ||
| def checks_ignored = 0 | ||
| def checks = 0 | ||
| if (qual_data && qual_data.containsKey(metric) && !qual_data[metric].status) { | ||
| reisolate = 1 | ||
| resequence = 1 | ||
| failed_p = true | ||
| checks_failed = 1 | ||
| }else if (qual_data && (!qual_data.containsKey(metric) || !qual_data[metric].status)) { | ||
| checks_ignored = 1 | ||
| }else if (qual_data == null) { | ||
| checks_ignored = 1 | ||
| } | ||
| checks += 1 | ||
| return [checks, reisolate, resequence, failed_p, checks_failed, checks_ignored] | ||
| } | ||
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| static def autofail_reisolate(java.util.LinkedHashMap qual_data, java.lang.String metric, java.util.ArrayList qc_message) { | ||
| def reisolate = 0 | ||
| def resequence = 0 | ||
| def failed_p = false | ||
| def checks_failed = 0 | ||
| def checks_ignored = 0 | ||
| def checks = 0 | ||
| if (qual_data && qual_data.containsKey(metric) && !qual_data[metric].status) { | ||
| reisolate = 1 | ||
| resequence = 1 | ||
| failed_p = true | ||
| checks_failed = 1 | ||
| }else if (qual_data && (!qual_data.containsKey(metric) || !qual_data[metric].status)) { | ||
| checks_ignored = 1 | ||
| }else if (qual_data == null) { | ||
| checks_ignored = 1 | ||
| } | ||
| checks += 1 | ||
| return [checks, reisolate, resequence, failed_p, checks_failed, checks_ignored] | ||
| } | ||
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| } | ||
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Could you add a
defaultcase 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).There was a problem hiding this comment.
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fixed in: e67cbdd