Orphanet benchmark #8
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…to be used for benchmarking. Also updated requirements.txt and setup.py to include xmltodict library because XML is a pain and I would rather work with json :)
maximusunc
requested changes
Sep 15, 2023
There was a problem hiding this comment.
Hi Greg, if you're still interested in getting this benchmark merged in, could you please fix the current merge conflicts with the main branch? I'd also like to request that you remove the additional python requirements from requirements.txt and setup.py. The reason behind that is that any data generation scripts are specific to those datasets and someone running the benchmarks doesn't need xmltodict in order to run the tests. We could maybe make a requirements-dev.txt that contained any requirements that individual dataset generation scripts need?
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Added a benchmark for OrphaNet containing rare-disease to gene edges. This includes a parser script to generate the data file from either the raw xml (en_product6.xml) or from http://www.orphadata.org/data/xml/en_product6.xml. We added a library to the setup.py and requirements.txt (xmltodict) to parse xml into python objects for ease. data.tsv includes the output benchmark edges that maps to our templates.