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Remove src_cd column (10th) in subj. sample file. #64

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@forus forus commented Mar 24, 2016

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@@ -53,7 +53,8 @@ class AssayStepsConfig implements StepBuildingConfigurationTrait {
delimiter: DELIMITER_TAB,
names: ['studyId', 'siteId', 'subjectId', 'sampleCd',
'platform', 'sampleType', 'tissueType', 'timePoint',
'categoryCd', 'source_cd'],
'categoryCd'],
strict: false
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Setting strict to false seems to olax:

Public setter for the strict flag. If true (the default) then number of
in line must match the number of tokens defined
{@link Range}, columns, etc.) in {@link LineTokenizer}.
false then lines with less tokens will be tolerated and padded with
columns, and lines with more tokens will
simply be truncated.

So ot will also tolerate missing columns. And it will of course not only ignore source_cd but any number of extra columns, with any name. I think it's better to implement a TokenizerColumnsReplacingHeaderHandler, like it's done for clinical data.

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Current coverage is 69.10%

Merging #64 into master will increase coverage by +0.02% as of 6ab170d

@@            master    #64   diff @@
=====================================
  Files          291    291       
  Stmts         4542   4558    +16
  Branches      1120   1125     +5
  Methods          0      0       
=====================================
+ Hit           3138   3150    +12
- Partial        758    762     +4
  Missed         646    646       

Review entire Coverage Diff as of 6ab170d

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@forus forus changed the title Ignore src_cd column (10th) in subj. sample file. Remove src_cd column (10th) in subj. sample file. Mar 25, 2016
@cataphract
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I think it's highly annoying that this breaks ALL the high dimensional data sets out there. An optional ignored source_cd column, with a warning/deprecation notice would be a much better transitional option.

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3 participants