LonnekeScheffer
commented
3 years ago Additional bugfixes added later:
- when accessing RepertoireDataset.metadata_file, this went wrong in galaxy because all files are replaced to a new folder. Due to this, it was impossible to run for example MatchedRegex encoder via Galaxy (which I was adding as an example to the docs). Added a check now that if the original metadata file path does not exist, but metadata file exists in the current working dir, that this then instead is returned.
- Some more flexibility in ExploratoryAnalysisParser that if a non-ML encoding is used, Labels do not have to be defined (it is very cumbersome to have to add fake labels to the data just to run a report that doesnt use labels), and moving a defaults file for matched_regex to the correct folder
All of this has been tested on my local galaxy instance
(sorry for the many e-mails, forgot to temporarily close the pull request)
This is a small bugfix; I thought the galaxy tools got a string in, but it actually already gets converted to a Path in immuneMLApp.py. Therefore, Galaxy currently fails due to an assertion error. This has been corrected here (tested successfully on local galaxy instance)