Is your feature request related to a problem? Please describe.
There is a lot of code in MMEDS dedicated to the handling of "sub-analysis" or "child analysis". This is generally handled inside config files, but not much is present besides the framework. Past this, we have been upgrading MMEDS without regard for these functionalities, and they are likely broken or incompatible with our current methods of analysis. However, we still need an easy way to do "sub-analysis", where we run an analysis tool on a specific subset of one study.
Describe the solution you'd like
A sub-analysis can simply be a type of meta-analysis that is contained to one study, i.e. if a meta-study query would have been WHERE SpecimenBodySite='Gut', the query for a sub analysis of the same kind for a given study ExampleStudy would be WHERE SpecimenBodySite='Gut' AND StudyName='ExampleStudy'. This will require only minor modifications to the current meta-analysis pipeline, most significantly allowing the sub-analysis to exist as a directory inside the original study directory. One specific change could be this: there is a boolean variable now meta_study that is true when a meta-study is being uploaded. Replace this with a variable study_type that can have values 'original', 'meta', or 'sub'.
Additional Context
The old child analysis code should be removed, which will be a significant improvement to codebase readability.
Is your feature request related to a problem? Please describe. There is a lot of code in MMEDS dedicated to the handling of "sub-analysis" or "child analysis". This is generally handled inside config files, but not much is present besides the framework. Past this, we have been upgrading MMEDS without regard for these functionalities, and they are likely broken or incompatible with our current methods of analysis. However, we still need an easy way to do "sub-analysis", where we run an analysis tool on a specific subset of one study.
Describe the solution you'd like A sub-analysis can simply be a type of meta-analysis that is contained to one study, i.e. if a meta-study query would have been
WHERE SpecimenBodySite='Gut', the query for a sub analysis of the same kind for a given study ExampleStudy would beWHERE SpecimenBodySite='Gut' AND StudyName='ExampleStudy'. This will require only minor modifications to the current meta-analysis pipeline, most significantly allowing the sub-analysis to exist as a directory inside the original study directory. One specific change could be this: there is a boolean variable nowmeta_studythat is true when a meta-study is being uploaded. Replace this with a variablestudy_typethat can have values 'original', 'meta', or 'sub'.Additional Context The old child analysis code should be removed, which will be a significant improvement to codebase readability.