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Correlations fail for at least some ProbeSet datasets (as the target dataset)


  • type: bug
  • priority: high
  • status: closed, completed
  • keywords: correlations


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Use the default dataset for correlation (the same as the trait)

You should get the following error:

GeneNetwork tux01:gene:2.11-rc2-gn_20221013-4eb4beafd 
    [Errno 2] No such file or directory: '/home/gn2/production/tmp/gn2/gn2/ProbeSetFreezeId_886_EPFL/ETHZ BXD Liver Proteome CD-HFD (Nov19)' (error)

This obviously has something to do with the sample data files, though not sure what yet.


I (fredm) was able to successfully reproduce the issue.

The issue here is that the code

generates the file name does not sanitize the input from the database, leading to issues with the final path.

In this case, the dataset name used to generate the file is (** Note the forward slash **):

EPFL/ETHZ BXD Liver Proteome CD-HFD (Nov19)

The following commit should fix the issue for most part:

(made with skribilo)