Differentiate between cancer study types for proteomics support

mikkonie commented 5 years ago

I noticed an issue with cancer study app shortcut generation in proteomics projects and discussed it with @mkuhring.

The "short" and "simple" version:

The cancer study app is used in a proteomics project, based on the bih_cancer configuration
It tries to find shortcut URLs in the study table per source but fails
This is actually OK, because data is (most likely) not sorted that way
Hence we are left with a useless shortcut column with buttons always disabled

Ergo, we'd need some way to (preferably) limit the use of the cancer study app to non-Proteomics projects, or at least tell the app not to provide shortcuts if it's used in a Proteomics project.

TBD: What parameter(s) to use in detecting the project type beyond ISAtab configuration? Or should there be a new configuration for cancer/proteomics?

Ideas are welcome.

mikkonie commented 5 years ago

Temporary workaround:

In the cancer study app:
Iterate through assays in study
IF only mass spec assays are found THEN don't show shortcuts (or create cache data for them)

mikkonie commented 5 years ago

mentioned in commit c161e017708fa14b3b13039df9f0a2f8166e2b89

mikkonie commented 5 years ago

Aforementioned workaround done for v0.5.0.

mikkonie commented 1 month ago

This should now be doable with the study plugin override feature implemented in #1885. Closing.

bihealth / sodar-server

Differentiate between cancer study types for proteomics support #482