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VEuPathDB / EdaNewIssues

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Are download files okay on mbio now? #570

Closed asizemore closed 3 months ago

asizemore commented 1 year ago

In previous releases we have had improperly formatted download files for mbio on the eda site, so we put up a warning about it in the downloads tab. Many of these studies (maybe all?) have been reloaded. Are these download files still improperly formatted?

As a reminder, here's an old github issue about the banner being put up.

asizemore commented 1 year ago

@SheenaTomko are you the right person to ask about this?

SheenaTomko commented 1 year ago

@asizemore I took a look at Bonus, where I first reported the issue, and that study looks good now. I think Dan should be glancing at all download files as part of his study qc, but I would guess that you can now remove the banner. One thing that threw me in Bonus though is that "Age" is somehow a key variable that is included in the participant repeated measure download by default, but it is also a variable, so you end up with the variable Age twice in that file. I'm not sure why Age is a key variable and how it ended up there, but I think only keys should be included in files by default. Not sure who that issue should be assigned to.

danicahelb commented 1 year ago

@SheenaTomko "Age" is a key variable because it is annotated as a mergeKey (ie, the key timepoint variable). We had decided that all repeated measures entity files should be forced to have a column with some sort of timepoint variable. But it should only be in there once... is this also happening in ClinEpi?

@asizemore there is this major issue with download files; I need advice as to what the mbio team wants to do about it: https://github.com/VEuPathDB/web-eda/issues/1652

Also, these mbio studies have too many files listed under “Full dataset” on the download tab:

  1. DIABIMMUNE
  2. FARMM
  3. Malaysia helminth study
  4. MORDOR phase I
  5. NICU NEC
  6. Preterm Infant Resistome I
  7. Preterm Infant Resistome II
  8. Uganda Maternal
  9. Bangladesh 5yr
  10. Bonus-CF
  11. HMP phase I (V3-V5)
  12. HMP phase I (WGS)
  13. PIH Uganda
asizemore commented 1 year ago

@danicahelb at this point it looks like the only problem remaining for this ticket to solve is the list of studies above that have too many download files? Is that correct?

asizemore commented 1 year ago

@danicahelb is this fixed? I just checked diabimmune and i think it looks good

aurreco-uga commented 3 months ago

seems fine