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clemente-lab / mmeds-meta

A database for storing and analyzing omics data
https://mmeds.org
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MMEDs analysis requires at least one metadata column #390

Open mstapylton opened 2 years ago

mstapylton commented 2 years ago

What parts of the analysis require a metadata column that has multiple values. Might be failing silently, not producing output if the criteria is not met

adamcantor22 commented 2 years ago

Not sure what you mean could you elaborate

cleme commented 2 years ago

Needs to be further clarified: is this a MMEDS issue, a QIIME issue, something else? Is this a bug? If so, provide way to reproduce it and assign to next release (unless it is a critical bug, in which case a patch is needed). If it is an enhancement, decide what release this should be placed in. In general, all issues should be created to be informative enough that they serve as a form of documentation on the project itself.

mstapylton commented 2 years ago

I think it's a MMEDS issue that manifests as a QIIME issue. I think it's an issue with how we create the jobfile in the case where only 1 column is specified. I need to investigate further to provide more details, it's not clear to me yet exactly what/where it's going wrong

cleme commented 2 years ago

Is it the issue running analysis with a single column, or running analysis on a column that has a single value? The latter is most likely to be an issue with QIIME, meaning: it will throw an error because there is only a single group, which is the desired behavior. So not really an issue, but a matter of having MMEDS capture that error even before the analysis starts, indicating more than one value is required to run certain analysis.

If the issue is happening with analysis using a single column but the column has multiple values, then it is most likely not a QIIME issue. So we need to clarify which one is it. If it is a MMEDS issue, then this will go into 0.8.0.

adamcantor22 commented 1 year ago

There are two issues here:

  1. MMEDS does not allow you to start an analysis with no metadata categories.
  2. When attempting to start an analysis with an invalid metadata column, a server error is thrown rather than a formatted error being presented to a user.

Solutions:

  1. Either allow no metadata categories (may be deceptively hard, there are likely lots of cases of looping over metadata categories) or replace the server error with a formatted one.
  2. Replace with a formatted warning and have the category be removed in code automatically, or replace with a formatted error.